Background: To estimate the relative risk of sexually transmitted infections (STIs) among children identified as having learning disabilities through the special education system. Methods: This cross-sectional study used special education data and Medicaid data from Philadelphia, Pennsylvania, for calendar year 2002. The sample comprised 51,234 Medicaid-eligible children, aged 12-17 years, 8015 of whom were receiving special education services. Claims associated with diagnoses of STIs were abstracted, and logistic regression was used to estimate the odds of STI among children in different special education categories. Results: There were 3% of males and 5% of females who were treated for an STI through the Medicaid system in 2002. Among females, those in the mental retardation (MR) category were at greatest risk (6.9%) and those in the emotionally disturbed or "no special education" category at lowest risk (4.9% each). Among males, STIs were most prevalent among those classified as mentally gifted (6.7%) and lowest among those in the MR category (3.0%). In adjusted analyses, males with specific learning disabilities and females with MR or who were academically gifted were at excess risk for STIs. Conclusions: The finding that children with learning disabilities are at similar or greater risk for contracting STIs as other youth suggests the need to further understand their risk behaviors and the potential need to develop prevention programs specific to their learning needs. (Contains 3 tables and 1 figure.)