Some research suggests that GI symptoms seen in children with ASD may relate to behavior problems. The objective of this pilot study was to assess the effect of the low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet on GI and behavioral problems in children with ASD. At follow-up, the low FODMAP diet group had significant relief in some GI problems compared with both baseline in the group and control group. At baseline and at follow-up, there were no significant differences in behavioral problems between the low FODMAP diet group and the control group. Randomized controlled studies including larger sample sizes are needed to confirm the effects of low FODMAP diets in children with autism who have gastrointestinal problems.