Neuromuscular deficits described in early childhood as motor awkwardness or slow movements are still clinically present in school-aged boys with XXY and XYY sex chromosome aneuploidy. A control group of 14 boys (6 to 19 years of age) and 14 XXY and four XYY boys (6 to 15 years of age), identified by newborn screening, were blindly evaluated by a physical therapist. The Bruininks-Oseretsky Test of Motor Proficiency (BOTMP) was administered and a clinical rating of neurologic status and sensory-motor integration was assigned. On the motor proficiency test, the XXY boys had significantly lower mean scores for upper limb coordination, speed and dexterity, and on gross motor and battery composites. The neuromuscular status of the aneuploid boys was deficient, with hypotonia, apraxia, primitive reflex retention, and problems with bilateral coordination and visual-perceptual-motor integration. This mild to moderate dysfunctional sensory-motor integration, as well as previously described auditory-processing deficits and dyslexia, contributed to school performance below that expected from their cognitive potential.