Investigate the association between gastrointestinal (GI) issues and psychometric scores among children with developmental delays and typical development. We examined the association between GI issues and the Mullen Scale of Early Learning (MSEL), Vineland Adaptive Behavior Subscales (VABS), and Aberrant Behavior Checklist (ABC) scores from participants with autism spectrum disorder (ASD), Down syndrome (DS), other developmental delays (DD) and typical development (TD) from the CHildhood Autism Risk from Genetics and Environment (CHARGE) Study (n = 1603). Approximately 32% of children with ASD, 31% of children with DD, and 20% of children with DS reported at least one GI issue, compared to 7% of TD controls. Constipation was the most frequently reported symptom for the entire population, including controls. In general, GI issues correlated with poorer behavioral scores (decreased communication, daily living, socialization, and motor skills on the VABS, and increased irritability/agitation, lethargy/social withdrawal, stereotypic behavior, and hyperactivity/noncompliance on the ABC) among ASD cases. Analysis by sex indicated that GI issues also correlated with poorer cognitive scores (fine motor, receptive language, expressive language, and MSEL composite scores), and adaptive behavior (communication skills, daily living skills, motor, and VABS composite scores) among boys with DD, but not girls with DD--suggesting sex differences among DD cases. Even TD controls showed increased stereotypic behavior and social withdrawal in association with GI issues. However, GI issues were not correlated with impairments in psychometric scores among DS cases. Given that GI issues correlate with deficits in behavioral and cognitive scores, future studies should investigate the treatment of GI symptoms in children with ASD and DD.