Objective: Microsatellite instability (MSI) in gastric cancer contributes to genetic complexities of gastric cancer. In the current study, we employed a panel of mononucleotide and dinucleotide markers to detect MSI in 99 gastric cancer patients and 91 chronic gastritis patients and further analyzed the association of MSI with clinicopathologic variables of the study patients. Methods: We retrospectively analyzed the clinicopathologic data of primary gastric cancer patients and chronic gastritis patients. MSI was analyzed using five microsatellite markers, including D2S12, D5S346, D17S799, BAT26, and D18S34. MSI was defined as either a band shift or the appearance of a novel band in DNA. Multivariate logistic regression analysis was used to predict risk of MSI. Results: Seventeen (17.2%) gastric cancer patients and 7 (7.7%) chronic gastritis patients were positive for MSI (P=0.012). Multivariate analysis further showed that gastric cancer was associated with a significantly higher likelihood for MSI versus gastritis (OR 3.73; 95% CI 1.19, 11.72; P=0.024) while age, drinking or smoking was not associated with increased MSI. Conclusion: Gastric cancer is associated with a high rate of MSI. MSI should be further explored in future studies with a larger sample size for its role in gastric cancer development and as a predictive biomarker.