Fragile X syndrome (FXS) and autism spectrum disorders (ASD) are characterized by impaired social functioning. We examined the spontaneous discrimination of happy and disgusted facial expressions, from neutral faces, in individuals with FXS (n = 13, Mage = 19.70) and ASD (n = 15, Mage = 11.00) matched on adaptive behavior and verbal abilities measured by the Vineland Adaptive Behavior Scale. Eye gaze to the eyes and mouth of neutral faces was also measured. Results suggest individuals with FXS and ASD distinguish facial expressions spontaneously in the same way. Individuals with FXS looked significantly less at the eye region of neutral faces than individuals with ASD. These results provide insight into similarities and differences in face processing in two neurodevelopmental disorders noted for their similarities in social behavior.