Abstract Early screening studies of autistic individuals suggested that up to one-quarter of cases were associated with the Fragile X anomaly. Recent studies find that the usual behavioural phenotype of the Fragile X anomaly is distinct from autism as usually defined, and that a variety of methodological factors contribute to the variability of the prevalence estimates. We report the prevalence of the Fragile X anomaly, using strict cytogenetic criteria, in a large sample of autistic individuals whose diagnosis was confirmed using a standardised diagnostic instrument. The anomaly was detected in 1.6% of tested autistic individuals from a combined sample of: autistic twins; clinic attenders; and, individuals from families multiplex for autism or related cognitive phenotypes. The anomaly was not detected in greater than 2.5% of any of the constituent samples and accounted for only a small proportion of the genetic influences amongst concordant twins and multiplex families. The anomaly was detected in 5% of the 40 tested autistic females, confirming reports that the prevalence of the anomaly is similar amongst autistic individuals of both sexes.