The phenomenon of anticipation has been demonstrated in several neuropsychiatric disorders and suggested for schizophrenia and bipolar affective disorder. Many conditions exhibiting anticipation have been shown to be caused by trinucleotide repeat (CAG/CTG) expansions. Some evidence suggests that these expansions also exist in individuals with schizophrenia and bipolar affective disorder. In this investigation, we analysed a polymorphic CAG repeat in the interleukin receptor gene (IL9R), mapped to the pseudoautosomal region Xq28 and Yq21 (a candidate region for schizophrenia and affective disorder). Two common alleles, differing by one repeat unit and two rare alleles were found in cases and controls. Allele frequencies of this repeat were investigated in Irish schizophrenic, bipolar disorder and ethnically matched control samples. We found no evidence of an increased frequency of larger CAG repeats in either the schizophrenic or bipolar affective disorder samples as a whole when compared to the controls. However, dividing the samples by sex demonstrated a significant association between bipolar affective disorder males and the larger allele (allele 2) (patients 54.8% vs controls 40.1%, chi2 = 6.7, P = 0.009). In addition, a decreased frequency of this allele has been observed in the female patients, but did not attain statistical significance (patients 37% vs controls 46%, chi2 = 2.1, P = 0.14). This provides preliminary evidence that this locus or a closely mapped DNA variant (in linkage disequilibrium with the CAG repeat) may be involved in the genetic susceptibility to bipolar affective disorder in males.