This study used a large administrative data set of Head Start programs across the United States, the Head Start Program Information Report (PIR), to explore disparities in program rates of screening, referral, and identification for early intervention between Migrant and Seasonal Head Start (MSHS) and Head Start (HS) programs. Results from program-level analyses of MSHS and HS disparities showed that MSHS programs screened more children but referred and identified fewer children. Disparities in identification persisted even in the presence of demographic controls and matching on key demographics. Post hoc sensitivity analyses showed that MSHS identification rates were negatively moderated by rurality. Implications to inform policymaking related to early intervention and preschool for children with or at risk for disabilities and dual language learners in rural Head Start programs are discussed.