Previous studies suggest over half of children with autism are using complementary alternative medicine (CAM). In this study, physicians responded (n = 539, 19% response rate) to a survey regarding CAM use in children with autism. Physicians encouraged multi-vitamins (49%), essential fatty acids (25%), melatonin (25%) and probiotics (19%) and discouraged withholding immunizations (76%), chelation (61%), anti-infectives (57%), delaying immunizations (55%) and secretin (43%). Physicians encouraging CAM were more likely to desire CAM training, inquire about CAM use, be female, be younger, and report greater autism visits, autism education and CAM knowledge. Physicians were more likely to desire CAM training, inquire about CAM and view CAM as a challenge for children with autism compared to children with other neurodevelopmental and chronic/complex conditions.