An autism module was added to an existing computer decision support system (CDSS) to facilitate adherence to recommended guidelines for screening for autism spectrum disorders in primary care pediatric clinics. User satisfaction was assessed by survey and informal feedback at monthly meetings between clinical staff and the software team. To assess outcomes, such as changes in identification and referrals, we reviewed data captured from the CDSS. Between November 15, 2010 and July 26, 2012, 857 patients were eligible for screening. Of these, 66% (567/857) were screened as determined by the number of forms scanned into the system, of which 30% (171/567) had concerning Modified Checklist for Autism in Toddlers. However, pediatricians failed to respond to alerts for 73 children. Of the remaining 98 children, pediatricians felt 50 (68%) did not have an Autism spectrum disorder, 23 (32%) were referred for autism evaluation, eight (11%) were suspected but not referred and two (3%) were referred for audiology. Seventy percent of all users agreed that automation of the screening process helped them to adhere to recommended guidelines. Automating autism care into a CDSS resulted in moderate adherence to guidelines. Health information technology can facilitate the implementation of autism guidelines in busy pediatric clinics.