Background: Peritoneal lavage cytology has been regarded as the only reliable method detect free cancer cells in the abdominal cavity. However, there certainly are patients who experience peritoneal recurrences despite negative cytology. Methods: Using qRT-PCR analysis, mRNA levels of 9 candidate molecular markers were quantified in peritoneal lavage fluids of from 187 patients with gastric cancer and 30 benign disease controls. ROC curve analysis was conducted to compare accuracies of the candidate markers. The cut-off points were set at the highest values of the benign disease controls. We evaluated predictive values of molecular markers in peritoneal lavage fluids for peritoneal recurrence. Results: From the result of ROC curve analysis, synaptotagmin XIII (SYT13) and carcinoembryonic antigen (CEA) mRNA levels were identified as predictive markers for peritoneal recurrences (The AUC value, 0.771, 0.775, respectively). 162 patients who had no concomitant peritoneal metastasis and were negative for lavage cytology (P0CY0), 13 patients (8.2%) had peritoneal recurrences. Those with either positive SYT13 or CEA mRNA level in peritoneal lavage fluids had significantly shorter peritoneal recurrence-free survival times compared to those with negative (3-years peritoneal recurrence-free survival rates, 69.5% vs 95.6%; P = 0.0069 and 79.3% vs. 93.4%; P = 0.0211, respectively). By combination of SYT13 and CEA, patients with both markers-positive had the greatest prevalence of peritoneal recurrences. Moreover, the peritoneal recurrence free survival curves of the both markers-positive group approached to that of the positive for lavage cytology group. Univariate analysis revealed that both SYT13-positive and CEA-positive were prognostic factors for peritoneal recurrence (hazard ratio: 4.21 and 3.53, respectively). In the multivariable analysis, SYT13-positive was found to be statistically significant independent prognostic factors (hazard ratio: 3.84, 95% confidence interval 1.24-13.2, P = 0.0202). Conclusions:SYT13 and CEA levels in peritoneal lavage fluids accurately predict peritoneal recurrences in patients with P0CY0.