BACKGROUND: Postoperative nausea and vomiting (PONV) are common complications after anesthesia and surgery. This study was designed to compare the effects of palonosetron and ondansetron in preventing PONV in high-risk patients receiving intravenous opioid-based patient-controlled analgesia (IV-PCA) after gynecological laparoscopic surgery. METHODS: One hundred non-smoking female patients scheduled for gynecological laparoscopic surgery were randomly assigned into the palonosetron group (n = 50) or the ondansetron group (n = 50). Palonosetron 0.075 mg was injected as a bolus in the palonosetron group. Ondansetron 8 mg was injected as a bolus and 16 mg was added to the IV-PCA in the ondansetron group. The incidences of nausea, vomiting and side effects was recorded at 2 h, 24 h, 48 h and 72 h, postoperatively. RESULTS: There were no significant differences between the groups in the incidence of PONV during 72 h after operation. However, the incidence of vomiting was lower in the palonosetron group than in the ondansetron group (18% vs. 4%, P = 0.025). No differences were observed in use of antiemetics and the side effects between the groups. CONCLUSIONS: The effects of palonosetron and ondansetron in preventing PONV were similar in high-risk patients undergoing gynecological laparoscopic surgery and receiving opioid-based IV-PCA.