Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder where a high frequency of gastrointestinal disturbance (e.g., constipation and diarrhea) is reported. As large bowel fermentation products can have beneficial or detrimental effects on health, these were measured in feces of children with and without ASD to examine whether there is an underlying disturbance in fermentation processes in the disorder. Fecal samples (48 h) were collected from children with ASD (n = 23), and without ASD (n = 31) of similar age. Concentrations of short chain fatty acids, phenols and ammonia were measured. Fecal total short chain fatty acid concentrations were significantly higher in children with ASD compared to controls (136.6 ± 8.7 vs. 111.1 ± 6.6 mmol/kg). Moreover, when concentrations of fecal acetic, butyric, isobutyric, valeric, isovaleric and caproic acids were measured, all were significantly higher in children with ASD compared with controls except for caproic acid. The concentration of fecal ammonia was also significantly greater in ASD participants than controls (42.7 ± 3.3 vs. 32.3 ± 1.9 mmol/kg). Fecal phenol levels and pH did not differ between groups. Macronutrient intake, as determined from dietary records kept by caregivers, also did not differ significantly between study groups. Our results suggest fermentation processes or utilization of fermentation products may be altered in children with ASD compared to children without ASD.