Autism spectrum disorder (ASD) is characterized by psychiatric and behavioral comorbidities. The Child Behavior Checklist (CBCL) provides valid and well-established measures of emotional, behavioral, and social problems in children and adolescents. The aim of the present study was to verify whether emotional, behavioral, and social problems were modulated by ASD symptom severity, cognitive development, gender, and age by analyzing the CBCL in a large group of children and adolescents with ASD. The results show that around 30% of participants with ASD exhibited internalizing problems and only 6% externalizing problems, with males exhibiting more internalizing problems than females. No correlation was found between CBCL scores and indices of ASD severity. However, higher CBCL Total Problems scores were found in older children and in children with lower cognitive abilities. The detection of behavioral and emotional problems allows children with ASD to undergo specific and individualized treatment that takes into account their psychopathological problems.