Children with neurogenetic syndromes (NGS) experience comorbid challenging behaviors and psychopathology. We examined challenging behaviors in 86 toddlers and preschoolers across three NGS [Angelman syndrome (AS), Prader--Willi syndrome (PWS), and Williams syndrome (WS)] and 43 low-risk controls (LRC), using the Child Behavior Checklist for Ages 1½-5. Challenging behavior profiles differed across NGS, with generally elevated behaviors in AS and WS, but not PWS, relative to LRC. Withdrawn and autism spectrum symptoms were particularly elevated in AS. Although several profiles were similar to those previously reported in older children and adults, we also observed inconsistencies that suggest non-linear developmental patterns of challenging behaviors. These findings underscore the importance of characterizing early challenging behaviors to inform atypical phenotypic development and targeted intervention.