Males are more likely to be diagnosed with autism than females, and at earlier ages, yet few studies examine sex differences in screening. This study explored sex differences in psychometric properties, recommended cutoff scores, and overall scores of the Modified Checklist for Autism in Toddlers, Revised, with Follow-Up. Participants were 28,088 toddlers enrolled in four early detection of autism studies. Children (N = 731) at high likelihood for autism attended evaluations after screening and/or primary care clinician concern. Females were less likely to screen at high likelihood for autism at each stage of screening and therefore less likely to be invited for evaluations. Positive predictive value was significantly lower among females than males, but sensitivity was similar. False positive females were likely to have another developmental delay. Cutoff scores for males and females matched recommended guidelines. Final scores on the Modified Checklist for Autism in Toddlers, Revised, with Follow-Up did not differ between males and females diagnosed with autism, but did for the overall sample identified at high likelihood for autism. Our findings suggest that females are less likely to be referred for evaluations, but the Modified Checklist for Autism in Toddlers, Revised, with Follow-Up accurately identifies both males and females with autism at established cutoffs. Future research should examine methods to reduce false positive in females.