Background: Research suggests that children with Down syndrome may be at increased risk of having an autism spectrum disorder; however, previous studies have not utilized comprehensive, state-of-the-art diagnostic tools to address the question of comorbid autism and Down syndrome. Method: Comprehensive evaluations for autism were conducted in 20 2-year-old children with Down syndrome. The Autism Diagnostic Observation Schedule-Generic (ADOS-G) and the Autism Diagnostic Interview-Revised (ADI-R) were administered by experienced clinicians, who then determined if the child presented with significant symptoms of autism. Eighteen children participated in a follow-up evaluation at age 4 years. Results: Three children (15%) met criteria for an autism spectrum disorder at both time points, and two (10%) for autistic disorder. Case descriptions are provided. Several children presented with difficulties in communication and play, but did not show problems in core social relatedness. The ADOS-G, if used alone, over-identifies autism in toddlers with Down syndrome. Conclusions: Clinical judgement is critical in diagnosing autism in Down syndrome. Young children may show some signs of autism (particularly in the area of communication) and not have the disorder. Children who have comorbid Down syndrome and autism are particularly challenged, relative to their peers without autism.