This study assessed the relation between pre-intervention variables (cognition, socialization and communication) to outcome in young children with autism. Method Twenty five children with autism (20–32 months) were enrolled in intensive behavior intervention. The children were divided into groups based on their IQ scores and on the severity of their social interaction and communication deficits [per autism diagnostic observation schedule (ADOS) scores]. Six developmental-behavioral domains including, imitation, receptive language, expressive language, nonverbal communication skills, play skills and stereotyped behaviors were assessed at pre- and post-1 year of intervention times. Results Significant progress was noted in all the six developmental-behavioral domains after 1 year of intervention. Children with higher initial cognitive levels and children with fewer measured early social interaction deficits showed better acquisition of skills in three developmental areas, receptive language, expressive language and play skills. Both groups showed better progress in Receptive language skills. Better progress in expressive language was associated with the child's social abilities, while more significant progress in play skills was related to pre-intervention cognitive level. Conclusions These findings emphasize the importance of early intensive intervention in autism and the value of pre-intervention cognitive and social interaction levels for predicting outcome.