Although the American Academy of Pediatrics recommends screening for autism spectrum disorder (ASD) for all young children, disparities in ASD diagnosis and intervention in minority children persist. One potential contributor to disparities could be whether physicians take different actions after an initial positive screen based on patient demographics. This study estimated factors associated with physicians completing the follow-up interview for the Modified Checklist for Autism in Toddlers with Follow-up (M-CHAT-F), and referring children to diagnostic services, audiology, and Early Intervention (EI) immediately after a positive screen. Children seen in a large primary care network that has implemented universal ASD screening were included if they screened positive on the M-CHAT parent questionnaire during a 16–30 month well child visit (N = 2882). Demographics, screening results, and referrals were extracted from the electronic health record. Children from lower-income families or on public insurance were more likely to have been administered the follow-up interview. Among children who screened positive, 26% were already in EI, 31% were newly referred to EI, 11% were referred each to audiology and for comprehensive ASD evaluation. 40.2% received at least one recommended referral; 3.7% received all recommended referrals. In adjusted multivariable models, male sex, white versus black race, living in an English-speaking household, and having public insurance were associated with new EI referral. Male sex, black versus white race, and lower household income were associated with referral to audiology. Being from an English-speaking family, white versus Asian race, and lower household income were associated with referral for ASD evaluation. A concurrent positive screen for general developmental concerns was associated with each referral. We found low rates of follow-up interview completion and referral after positive ASD screen, with variations in referral by sex, language, socio-economic status, and race. Understanding pediatrician decision-making about ASD screening is critical to improving care and reducing disparities.