Variability in clinical expression and in intervention outcome has been described in autism spectrum disorder (ASD). The study examined progress after 1 and 2 years of intervention and compared the impact of baseline cognitive ability on outcome trajectories in 46 children (m = 25.5 months) with ASD. The entire group showed a gradual decrease in autism severity and increase in verbal cognitive scores. Only the low cognitive scores (DQ <70) group significantly improved in fine motor and receptive language scores. Significant gains in adaptive skills were found only for the high cognitive scores (DQ ≥70) group after 2 years of intervention. The entire group progressed with intervention, but only children with higher cognitive levels at baseline transferred their acquired socio-communication skills into daily functioning.