We performed a pharmacogenetic study to analyse the correlation between the clinical responses to ondansetron during a 24-h postoperative period and two single nucleotide polymorphisms (-100_-102 delAAG and ins/delCA) in the serotonin receptor type 3B gene (HTR3B) in 280 Korean patients with tonsillectomy (TS, n=108) or surgery because of gynaecological problems (GY, n=172). The effect of CA/CA homogyzous variant of the ins/delCA allele on lowering the prevention of postoperative vomiting was significant, particularly during the initial 2 h postoperative period (P=0.034) and in the GY group (P=0.013 for complete response and P=0.009 for prevention of vomiting). However, we failed to detect a significant effect of genotypes for the -100_-102delAAG allele during our observation period. Our results suggest that ins/delCA polymorphism in the HTR3B may have clinical relevance to the expected clinical response to prevent postoperative vomiting in patients treated with ondansetron.