Seven single nucleotide polymorphisms (SNPs) present on 13q32 were detected among 124 British family trios consisting of fathers, mothers and affected offspring with schizophrenia. The transmission disequilibrium test (TDT) demonstrated that of these 7 SNPs, rs626716, a T to C base change at the KPNB3 locus, was the only SNP associated with schizophrenia (chi(2) = 7.71, P = 0.005) although the global P-value given by a permutation test was 0.04 for 100 permutations. Of 248 parents, 20 were heterozygous. These heterozygous parents had transmitted 4 T-alleles and 16 C-alleles to their affected offspring. To further validate the rs626716 association, we analysed a haplotype system composed of 3 SNPs at the KPNB3 locus. The result showed that the KPNB3 haplotypes were also associated with schizophrenia (chi(2) = 10.18, d.f. = 2, P = 0.006). Because the KPNB3 finding has been replicated in a Chinese population, it could be hypothesized that the KPNB3 locus may contain a disease-causing variant for schizophrenia.