An atypical presentation of autism spectrum disorder is noted in Cornelia de Lange and Fragile X syndromes, but there are few detailed empirical descriptions. Participants in this study were individuals with Cornelia de Lange syndrome (n = 130, M age = 17.19), Fragile X syndrome (n = 182, M age = 16.94), and autism spectrum disorder (n = 142, M age = 15.19), who were comparable on chronological age. Using the Social Communication Questionnaire, the proportion meeting cutoff for autism spectrum disorder and autism was 78.6%, and 45.6%, respectively, in Cornelia de Lange syndrome and 83.6% and 48.6% in Fragile X syndrome. Domain and item analyses indicate differing, atypical autism spectrum disorder profiles in Fragile X and Cornelia de Lange syndromes. A limited association between adaptive behavior and autism spectrum disorder was identified in all groups. The findings have implications for intervention in genetic syndromes and conceptualization of autism spectrum disorder in the wider population.