Background: Previous studies suggested that children diagnosed with fragile X syndrome (FXS) often meet criteria for autism or PDD. This study describes the fine motor abilities of children diagnosed with FXS with and without autism spectrum disorder, and compares the motor scores of those groups controlling for cognitive level. Method: Forty-eight children, ages 12-76 months (SD = 16) diagnosed with FXS were assessed with the Mullen Scales of Early Learning, and the Autism Diagnostic Observation Schedule. Their parents were interviewed with the Autism Diagnostic Interview-Revised. We used a one-way analysis of variance to determine if the fine motor scale of the Mullen would show group differences based on autism classifications for the sample. In addition, we used Pearson correlation coefficient to examine the relationship between the cognitive level, the autism severity and the motor abilities. Lastly, we conducted a one-way analysis of covariance to determine the difference between the motor abilities of the Autism Spectrum Disorder groups controlling for cognitive level. Results: We found that 60% of the children with FXS met criteria for autism or Pervasive Developmental Disorder-Not otherwise specified (PDD-NOS). Children with FXS with autism and PDD-NOS had lower fine motor scores than those without. However, there was no significant association between degree of motor impairment and communication and social impairments after controlling for cognitive level, indicating that cognitive level contributes to impaired motor abilities of children diagnosed with FXS and autism, more than the severity of autism symptoms. Conclusion: Children with FXS and autism are at risk for impaired motor abilities. Implications for development and intervention are discussed.