Numerous studies have shown there is consistent evidence implicating genetic factors in the etiology of autism. In some cases chromosomal abnormalities have been identified. One type of these abnormalities is gaps and breaks nonrandomly located in chromosomes, denominated fragile sites (FS). We cytogenetically analyzed a group of autistic individuals and a normal population, and we examined the FS found in both samples with the aim of (1) comparing their FS expression, (2) ascertaining whether any FS could be associated with our autistic sample, and (3) examining if there are differences between individual and pooled-data analyses. Different statistical methods were used to analyse the FS of pooled and individual data. Our results show that there are statistically significant differences in the spontaneous expression of breakages between patients and controls, with a minimal sex difference. Using the method for pooled data, eight autosomal FS have preferential expression in patients and five patients were found to be positive at FS Xq27.3. With the method per-individual analysis, four FS emerged as specific in our autistic sample. Inferences of FS from pooled data were different from those of individual data. The findings suggest that although analysis of pooled data is necessitated by the problem of sparse data, analysis of single individuals is essential to know the significance of FS in autism.