Background: People with autism spectrum disorder (ASD) can experience affective problems, gastrointestinal (GI) symptoms, sleep problems, and challenging behaviour. This study identified the frequency of affective problems and explored how they related to co-occurring conditions in children and adolescents with ASD. Method: Participants were children and adolescents diagnosed with ASD using DSM-IV-TR criteria (n = 95), 40 % (n = 38) of whom also had a diagnosis of intellectual disability (ID). The following scales were completed by the participants' parents or guardians: Child Behaviour Checklist (CBCL), Gastrointestinal Symptoms Inventory, Children's Sleep Habits Questionnaire (CSHQ), and the Behaviour Problems Inventory-Short Form (BPI-S). Pearson's correlations and independent sample t-tests were used to examine the relationships between variables. Two hierarchal multiple regressions examined predictors for affective problems in preschool and school-aged children with ASD. Results: Participants scored in the clinical range (69.5 %) and borderline range (10.5 %) for affective problems. Significant positive relationships were found between affective problems and sleep problems, GI symptoms, and challenging behaviour. ID and gender predicted affective problems in preschool aged children. In school-aged children, affective problems were predicted by ID, sleep problems, and aggressive/destructive behaviour severity. However, only 25 % of the variance in affective problems was accounted for. Conclusions: Future research is needed to understand how affective problems are impacted by cooccurring conditions in children and adolescents with ASD. Affective problems are prevalent in this population and the quality of life for individuals may be improved if practitioners consider co-occurring conditions during clinical practice.