Motor skills, an important foundation for language and communication, are considerably delayed in children with Down syndrome (DS) and fragile X syndrome (FXS). However, the impact of these impairments on expressive and receptive communication and the phenotypic specificity of these associations remains unknown. Participants included 37 with DS and 37 age and developmentally matched children with FXS. Syndrome-specific motor and communication profiles emerged, with higher communication scores seen in the DS versus FXS on, but lower gross motor scores. Significant associations between domains of motor and communication were identified for both groups with additional phenotype-specific patterns. Findings demonstrate the importance of early motor abilities for communication in DS and FXS. Implications for phenotypic specificity and targeted intervention are discussed.