Studies have shown that Autism Spectrum Disorder (ASD) screening and diagnostic instruments may be affected by the presence of emotional and behavior problems (EBPs). This study assessed the impact of EBPs on the Modified Checklist for Autism in Toddlers, Revised with Follow-up (M-CHAT-R/F). Participants included 290 children, 18-48 months of age, referred for ASD-related concerns. Those diagnosed with ASD had significantly lower externalizing EBPs compared to those who were not diagnosed with ASD. More externalizing symptoms and younger age were significantly predictive of an M-CHAT-R/F final score. Sensitivity and specificity was impacted by the age of the child. These results suggest that combining measures that assess EBPs and autism core symptoms may improve accuracy in this referred population.