Individuals with intellectual disability (ID) show high rates of challenging behavior (CB). The aim of this retrospective study was to assess the factors underlying CB in an adult, clinical ID sample (n = 203). Low levels of emotional development (ED), as measured by the Scheme of Appraisal of ED, predicted overall CB, specifically irritability and self-injury, high unemployment and low occupation rates, while severity of ID controlled for ED did not. Autism was the only mental disorder associated with overall CB, stereotypy, lethargy, and predicted antipsychotic drug usage. Given the persistence and clinical significance of CB, evaluation of autism and ED may suggest priority areas for diagnostics and therapy, to provide the prerequisites for participation in society and living up one’s potentials.