This study examined whether secondary medical diagnoses that affect CNS function (i.e., seizures, malformations, or genetic disorders), are more likely to occur in individuals with fragile X syndrome (FXS) and autism spectrum disorder (FXS + ASD) or FXS alone. Ninety males (3–25 years) with FXS or FXS + ASD were evaluated for secondary medical diagnoses by medical history and examination. A significant difference in the incidence of medical problems was found between patients with FXS + ASD (38.6%) and FXS alone (18.2%, P < 0.05). Medical problems that affect the CNS are more likely to occur in those with FXS + ASD and it is probable that additional brain dysfunction associated with these medical problems enhance the risk of autism in those with FXS. © 2008 Wiley‐Liss, Inc.