Recently, case-control studies have suggested an association between the polymorphic CAG repeat in the neuronal potassium channel gene hSKCa3 and an increased susceptibility to schizophrenia, with larger repeats being overrepresented in schizophrenic patients. Therefore, we have examined the CAG repeat polymorphism in hSKCa3 and four adjacent microsatellite markers in 12 multiplex schizophrenia families. On performing the extended transmission/disequilibrium test (ETDT), neither allele-wise (P = 0.67) nor genotype-wise (P = 0.071) analysis yielded evidence to support linkage disequilibrium between schizophrenia and the hSKCa3 CAG repeat alleles. No significant results were produced performing parametric and non-parametric linkage analysis between schizophrenia and hSKCa3, as well as the four microsatellite markers. Thus, our study does not support the involvement of hSKCa3 in schizophrenia. Furthermore, we refined the physical localization on chromosome 1q21.3 using linkage analysis. No recombination was seen between markers D1S2624 and D1S1600 and the polymorphic CAG repeat in hSKCa3. LOD scores of 19.44 and 12.97, respectively, were obtained at a recombination fraction of 0.00.