This retrospective study examined predictors of outcome for children with autism following 6 and 12 months of early intensive behavioral intervention. Potential predictor variables included pretreatment functioning, age at onset of treatment, treatment intensity, family involvement, and physical characteristics (e.g., brain abnormalities, dysmorphology). For the 19 study participants, presence of dysmorphic features was the only variable that predicted response to treatment after 6 months (R-squared = .58). Dysmorphology was associated with worse outcomes. After 12 months, both dysmorphology and a history of regression predicted poorer response to treatment (R-squared = .67). Children who made the most progress in treatment had pretreatment language skills and normal physical features. Dysmorphic features in children with autism may represent abnormalities in prenatal development that are associated with poorer child outcomes.