This study aimed at analyzing the differences in challenging behaviors between adults with intellectual disability and ASD and those who only had intellectual disability, as well as to explore associations between transdiagnostic and clinical variables to these differences. Therapists and educators of 163 adults with intellectual disability (83 with additional ASD diagnosis) completed the test battery. Mean difference analysis and univariate analyses of covariance were performed to determine the impact of clinical variables and transdiagnostic variables on the frequency and severity of challenging behaviors. Results showed that adults with ASD and intellectual disability presented higher frequency and severity of these behaviors. A significant effect of the diagnosis of ASD on the frequency and severity of self-injuries and stereotypies was found. Also, some transdiagnostic variables influencing the presence of these behaviors were highlighted. These factors should be considered when planning and designing interventions for behavioral problems in this population.