The poor levels of fitness in children with autism are prompting concern for the children's future health. This study looked to assess if a computer-based activity programme could improve fitness levels (as reflected in cardiopulmonary function) of these children, and achieve a reduction in their body mass index. In a randomised controlled trial, 50 children with autism (of which 33 were under the age of 11 years and 39 were boys) were allocated to an intervention group which encouraged them to use the Nintendo Wii and the software package "Mario and Sonics at the Olympics" in addition to their routine physical education classes. 50 children with autism (34 under the age of 11 years and 40 being boys) acted as controls. At the end of one year, analysis of the changes in scores using analysis of covariance (ANCOVA) on the Eurofit fitness tests showed that the intervention group had made statistically significant improvement on all tests other than flexibility. These improvements were also significantly better than controls. This type of intervention appears to be an effective addition to standard fitness training in order to help children with autism improve their fitness levels.