The serotonin type 3 (5-HT3) receptor (R) belongs to the family of ligand-gated ion channels. It is supposed to play an important role in the pathogenesis of schizophrenia and might also represent an interesting target for the pharmacological treatment of this disorder. In this study, we searched for variations within the 5-HT3A receptor gene which might be specifically associated to schizophrenia. Twenty-nine single nucleotide polymorphisms (SNPs) of 943 schizophrenic patients compared to 2,343 healthy individuals were analyzed. SNPs were selected taking into account previous results on a 5-HT3A receptor domain involved in neuroleptic binding. Dominant logistic and linear regression models were calculated for the phenotypes number of hospitalizations, duration of hospitalization, age at onset and case–control. The data did not show significant associations of any SNP under investigation specific for schizophrenic patients. In conclusion, our study does not support the hypothesis that the 5-HT3A receptor plays a major role in the pathogenesis of schizophrenia. © 2012 Wiley Periodicals, Inc.