Optimal Clinical Coding for CYSHCN
Though electronic medical records have simplified diagnostic coding for many, understanding all available codes may support better billing and compensation, particularly for services provided to children and youth with special health care needs (CYSHCN). Some codes may not be recognized or compensated by some insurers, but codes that are used appropriately are more likely to gain recognition and compensation over time. In larger organizations, coding for all services rendered may result in additional work relative value units (WRVU) credited to clinicians, even if they do not result in third-party payment.
International Classification of Diseases (ICD-10) Coding
Diagnosis coding is based on the ICD-10-CM (International Classification of Diseases, Tenth Revision, Clinical Modification), which includes codes that describe diagnoses, conditions, signs, and symptoms. It also has codes for injuries, poisoning, and other external causes of morbidity (such as accidents and exposures) and factors influencing health status and contact with health services. The Centers for Disease Control and Prevention (CDC) maintain an updated, free version of the International Classification of Diseases, 10th Revision (WHO); ICD10Data.com offers a free, user-friendly way to search for codes.
ICD-10 code books are organized in two ways—alphabetically by diagnosis (Index) and numerically by code (Tabular List). In general, first look in the alphabetic list for the diagnosis, symptom, etc. Then look up that code in the tabular list to confirm its accuracy and to peruse subcodes and surrounding codes to ensure appropriate specificity and level of detail.
The most specific code(s) possible should be used.
Example
Q20-28 Congenital malformations of the circulatory system
- Q21 Congenital malformations of cardiac septa
- Q21.3 Tetralogy of Fallot
Example
H65-H75 Diseases of middle ear and mastoid
- H66 Suppurative and unspecified otitis media
- H66.00 Acute suppurative otitis media without
spontaneous rupture of eardrum
- H66.004 Acute suppurative otitis media without spontaneous rupture of ear drum, recurrent, right ear
- H66.00 Acute suppurative otitis media without
spontaneous rupture of eardrum
ICD-10 Diagnostic Coding for Unknown Diagnoses
- Fever [R50.9]
- Hemoglobinuria [R82.3]
- Macrocephaly [Q75.3]
- Low-birth weight, 1500-1999 grams [P07.17]
- Routine child health check with abnormal findings [Z00.121]
- Fall from non-moving wheelchair, initial encounter [W05.0XXA]
ICD-10 Diagnostic Coding for Social Determinants of Health
Social Determinant | ICD-10-CM code/description |
Abuse (history of) | Z62.810 Personal history of physical and sexual abuse in
childhood Z62.811 Psychological abuse in childhood Z62.812 Neglect in childhood Z62819 Unspecified abuse in childhood |
Economic difficulties | Z59.5 Extreme poverty Z59.6 Low income Z59.7 Insufficient social insurance and welfare support Z91.120 Patient’s intentional underdosing of medication regiment due to financial hardship |
Education | Z55.1 Schooling unavailable and unattainable
Z55.3 Underachievement in school Z55.4 Educational maladjustment and discord with teachers and classmates |
Environmentally compromised housing | Z77.011 Contact with and (suspected) exposure to lead
Z77.1 … to other environmental pollution |
Family/primary support group issues (relationship) | Z63.31 Absence of family member due to military
deployment Z63.4 Disappearance and death of family member Z63.5 Disruption of family by separation and divorce Z63.71 Stress on family due to return of family member from military deployment Z63.79 Other stressful life events affecting family and household Z63.0 Problems in relationship with spouse or partner |
Food insecurity | Z59.4 Lack of adequate food |
Parent/sibling-child issues | Z62.0 Inadequate parental supervision and control
Z62.3 Hostility toward and scapegoating of child Z62.6 Inappropriate (excessive) parental pressure Z62.820 Parent-biological child conflict Z62.821 Parent-adopted child conflict Z62.822 Parent-foster child conflict |
Social issues | Z60.0 Problems of adjustment to life-cycle transitions
Z60.3 Acculturation difficulty Z60.4 Social isolation, exclusion and rejection Z60.5 Target of (perceived) adverse discrimination and persecution |
Substance use | Z63.72 Alcoholism and drug addiction in family
Z71.41 Alcohol abuse counseling and surveillance of alcoholic Z71.42 Counseling for family member of alcoholic Z71.51 Drug abuse counseling and surveillance of drug abuser Z71.52 Counseling for family member of drug abuser |
Transportation issues | Z79.89 Other specified risk factors, not elsewhere classified |
Upbringing issues | Z62.21 Child in welfare custody Z62.22 Institutional upbringing Z62.29 Other upbringing away from parents Z62.898 Other specified problems related to upbringing Z62.9 Problem related to upbringing, unspecified |
Current Procedural Terminology (CPT) Coding
The codes used to bill for medical services are described by the CPT (Current Procedural Terminology) , published by the American Medical Association, and not available in a free version. It includes various categories and types of codes, but we will focus on Category 1 codes that are used for evaluation and management services in outpatient settings. Most of the codes described below apply to services provided by physicians. Some include services provided by other qualified health care professionals, defined as “individuals who are qualified by education, training, licensure/regulation (when applicable) and facility privileging (when applicable) who perform professional services within his/her scope of practice and independently reports that professional service.” This group includes nurse practitioners, certified nurse specialists, physician assistants, clinical social workers, physical therapists, and others. Some codes also include services provided by clinical staff under the supervision of a physician or another qualified health care professional.
Evaluation and Management Services
- Reviewing tests in visit preparation
- Counseling or educating a patient, family, or caregiver (including prolonged discussion related to misperceptions, information gathered from the internet, etc.)
- Reporting test results by phone
- Ordering medications, tests, or procedures
- Documenting related work at home
New Patients | |
99202 | 15-29 min. |
99203 | 30-44 min. |
99204 | 45-59 min. |
99205 | 60-74 min. |
99XXX | ≥ 75 min. |
Established Patients | |
99212 | 10-19 min. |
99213 | 20-29 min. |
99214 | 30-39 min. |
99215 | 40-54 min. |
99XXX | ≥ 55 min. |
- The number and complexity of problems addressed; it is no longer necessary to document all of a patient’s diagnoses, just those addressed during the encounter
- The amount and complexity of data reviewed and analyzed; it is no longer necessary to include irrelevant data in the encounter record
- Risk of complications or morbidity, including social determinants of health and reasons behind decisions to not intervene in some way
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Adolescent Confidentiality Related to Billing (AAP) (
615 KB)
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Adolescent Health Services Coding (AAP) (
79 KB)
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After-hours and Special Services Coding (AAP) (
84 KB) (urgent and when not regularly scheduled)
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Coding for Pediatric Preventive Care (AAP) (
2.0 MB)
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Oral Health Coding (AAP) (
223 KB)
- Osteopathic Manipulation Coding (AAP)
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Coding for Telemedicine Services (AAP) (
245 KB)
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Transition to Adult Health Care Coding - 2021 (AAP & GotTransition) (
426 KB)
- Various mental health/behavioral issues, including
ADHD Coding (AAP) (
149 KB) and Anxiety Coding (AAP) (
148 KB)
Medical Home Services

Care Plan Oversight Services
- The appropriate code is based on total time within a calendar month: 99339 (15-29 minutes) or 99340 (30 minutes or more).
Home Services
- For new patients, 99341-99345, with typical duration from 20 to 75 minutes
- For established patients, 99347-99350, with typical duration from 15 to 60 minutes

Prolonged Services With Direct Patient Contact
- 99354 is used for the first “hour” (30-74 minutes) of prolonged services; this code may be used only once for a given date.
- 99355 is used for each additional 30 minutes beyond the first hour (total of 75-104 minutes, 105-134 minutes, etc.) on a given date.
Prolonged Services Without Direct Patient Contact
- 99358 is used for the first “hour” (30-74 minutes) of prolonged services; this code may be used only once for a given date.
- 99359 is used for each additional 30 minutes beyond the first hour (total of 75-104 minutes, 105-134 minutes, etc.) on a given date.
Prolonged Clinical Staff Services With Physician or Other Qualified Health Care Professional Supervision
- 99415 is used for the first hour of prolonged clinical staff service
- 99416 is used for each additional 30 minutes beyond the first hour
COVID-19 Vaccine and Administration Services

CPT Code | Description |
91300 | Pfizer-BioNTech COVID-19 Vaccine Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]) vaccine, mRNA-LNP, spike protein, preservative free, 30 mcg/0.3mL dosage, diluent reconstituted, for intramuscular use. (Report 91300 with administration codes 0001A, 0002A) |
0001A | Pfizer-BioNTech COVID-19 Vaccine Administration by intramuscular injection of severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) (Coronavirus disease [COVID-19]) vaccine, mRNALNP, spike protein, preservative free, 30 mcg/0.3mL dosage, diluent reconstituted; first dose |
0002A | - administration of second dose of Pfizer-BioNTech vaccine |
91301 | Moderna COVID-19 Vaccine Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]) vaccine, mRNA-LNP, spike protein, preservative free, 100 mcg/0.5mL dosage, for intramuscular use. (Report 91301 with administration codes 0011A, 0012A) |
0011A | Moderna COVID-19 Vaccine Administration by intramuscular injection of severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) (Coronavirus disease [COVID-19]) vaccine, mRNALNP, spike protein, preservative free, 100 mcg/0.5mL dosage; first dose |
0012A | - administration of second dose of Moderna vaccine |
COVID-19 Testing


CPT Code | Description |
86328 | Immunoassay for infectious agent antibody(s), qualitative or semiquantitative, single-step method (e.g., reagent strip); |
86408 | Neutralizing antibody, severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2) (Coronavirus disease [COVID19]); screen |
86409 | - titer |
86413 | Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2)(Coronavirus disease [COVID-19]) antibody, quantitative |
86769 | Antibody; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 Coronavirus 2) (Coronavirus disease [COVID-19]) |
87426 | Infectious agent antigen detection by immunoassay technique, (e.g., enzyme immunoassay [EIA], enzyme-linked immunosorbent assay [ELISA], fluorescence immunoassay [FIA], immunochemiluminometric assay [IMCA]) qualitative or semiquantitative; severe acute respiratory syndrome coronavirus (e.g., SARS-CoV, SARS-CoV-2 [COVID-19]) |
87428 | Multiplex infectious agent antigen detection by immunoassay technique, (e.g., enzyme immunoassay [EIA], enzyme-linked immunosorbent assay [ELISA], fluorescence immunoassay [FIA], immunochemiluminometric assay [IMCA]) qualitative or semiquantitative; severe acute respiratory syndrome coronavirus (e.g., SARS-CoV, SARS-CoV-2 [COVID-19]) and influenza virus types A and B |
87635 | Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), amplified probe technique |
87636 | Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]) and influenza virus types A and B, multiplex amplified probe technique |
87637 | Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), influenza virus types A and B, and respiratory syncytial virus, multiplex amplified probe technique |
87811 | Infectious agent antigen detection by immunoassay with direct optical (i.e., visual) observation; severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]) |
Medical Team Conferences
- 99366 is used by nonphysician qualified health care professionals for participation in conferences of 30 minutes or more, with patient and/or family present.
- 99367 is used by physicians for participation in conferences of 30 minutes or more, with the patient or family not present. (Physicians should use E/M codes to report time in team conferences with the patient and/or family present.)
- 99368 is used by nonphysician qualified health care professionals for participation in conferences of 30 minutes or more, with patient or family not present.
General Behavioral Health Integration Care Management
Care Management Services
- 99487 is used for establishment/substantial revision of a comprehensive care plan involving moderate-high complexity medical decision-making requiring 60 minutes of clinical staff time in a calendar month
- 99489 is used to report each additional 30 minutes required in a calendar month
- 99490 is used for establishment, implementation, revision, or monitoring of a comprehensive care plan requiring at least 20 minutes of clinical staff time in a calendar month
- 99491 is used for establishment, implementation, revision, or monitoring of a comprehensive care plan requiring at least 30 minutes of physician or other qualified health care professional time in a calendar month
Principal Care Management (PCM) Services
- G2064. CCM for a single high-risk disease (i.e., PCM) at least 30 minutes of physician or other qualified health care professional time per calendar month
- G2065. CCM for a single high-risk disease, at least 30 minutes of clinical staff time directed by a physician or other qualified health care professional per calendar month
Transitional Care Management Services
- 99495 includes communication (direct contact, telephone, electronic) with the patient/caregiver within 2 business days and a face‐to‐face visit within 14 calendar days of discharge and medical decision‐making of at least moderate complexity
- 99496 includes communication (direct contact, telephone, electronic) with the patient and/or caregiver within 2 business days, a face‐to‐face visit within 7 calendar days of discharge, and medical decision‐making of high complexity
Telephone Services
- 99441 involves 5-10 minutes of medical discussion
- 99442 involves 11-20 minutes of medical discussion
- 99443 involves 21-30 minutes of medical discussion
Online Medical Evaluation
- 99421. Online digital E/M service, for an established patient, 5-10 minutes cumulative time over up to seven days
- 99422. Online digital E/M service, for an established patient, 11-20 minutes cumulative time over up to seven days
- 99423. Online digital E/M service, for an established patient, 21 or more minutes cumulative time over up to seven days
Interprofessional Telephone/Internet/Electronic Health Record Consultations
- 99446 involves 5-10 minutes of medical consultative discussion and review
- 99447 involves 11-20 minutes of medical consultative discussion and review
- 99448 involves 21-30 minutes of medical consultative discussion and review
- 99449 involves 31 minutes or more of medical consultative discussion and review
Education and Training for Patient Self-Management
- 98960 – an individual patient
- 98961 – 2-4 patients
- 98962 – 5-8 patients
Resources
Information & Support
Related Portal pages:
For Professionals
Medical Home Resources (AAP)
An in-depth look at the medical home model and how to implement it. Includes information about quality improvement, maintenance
of certification activities to improve your medical home, and financing and payment resources; American Academy of Pediatrics.
Coding Resources (AAP)
Books, quick references, and how-to guides for CPT and ICD-10 coding specific to pediatrics; available for purchase from the
American Academy of Pediatrics.
2022 Coding and Payment Tip Sheet for Transition from Pediatric to Adult Health Care ( 509 KB)
Thirty-two page booklet of CPT coding options for the provision of transition-related services; from Got Transition and the
American Academy of Pediatrics.
CPT (Current Procedural Terminology)
Link to the American Medical Association Store where the current version of the CPT can be purchased in hardcopy.
ICD10Data.com
Free, user-friendly reference website that contains all of the official American ICD-10-CM (diagnosis) and ICD-10-PCS (procedure)
medical billing codes.
Physician Fee Schedule Look-Up Tool (CMS)
Offers information on each CPT (aka Healthcare Common Procedure Coding System, HCPCS) code, including assigned relative value
units (RVUs), payment amounts (both national and by specific localities) and more; from the Centers for Medicare and Medicaid
Services (CMS)
Code/Reimbursement Lookup Tool (Utah Medicaid)
Allows determination of coverage and pre-authorization requirements, by provider type and service code; page includes link
to the full Utah Medicaid Fee Schedule.
Authors & Reviewers
Author: | Chuck Norlin, MD |
Contributing Author: | Jason Fox, MPA/MHA |
2020: update: Chuck Norlin, MDA; Jason Fox, MPA/MHACA |
2019: update: Jennifer Goldman, MD, MRP, FAAPA; Chuck Norlin, MDA; Joni A. Hemond, MD, FAAPCA; Wendy L. Hobson-Rohrer, MD, MSPH, FAAPCA; Jason Fox, MPA/MHACA; Jeremy Egusquiza, MBACA |
2018: update: Jennifer Goldman, MD, MRP, FAAPA |
2008: first version: Chuck Norlin, MDA |
Page Bibliography
AAP Division of Health Care Finance.
Use ICD-10-CM codes when social determinant of health identified.
American Academy of Pediatrics; (2021)
https://www.aappublications.org/news/2021/01/01/coding010121. Accessed on 1/21/2021.