Background Mitochondrial DNA 4977-bp deletion (△mtDNA4977) was reported in many human neoplasia. However, its biological significance remains to be evaluated and the molecular mechanism needs to be investigated. In this study, we analyzed the frequency of △mtDNA4977 in gastric cancer (GC) cell lines and tissues, as well as reactive oxygen species (ROS) contents and manganese superoxide dismutase (MnSOD) expression levels in GC cell lines to explore its biological significance and molecular mechanism.Methods Semi-quantitative PCR and real-time PCR were used to detect the incidence of △mtDNA4977 in 13 GC cell lines and 272 human gastric tissues (108 GC specimens and the respective adjacent normal tissues, and 56 normal gastric mucosa from non-cancer patients). We further identified intracellular ROS production by flow cytometry and MnSOD expression by semi-quantitative reverse transcription-PCR (RT-PCR) and West blotting. Statistical analyses were carried out using the Logistic regression analysis and Kaplan-Meier method.Results Based on our earlier study, we optimized the PCR amplification condition by reducing the cycle number. In this study, we systematically documented the high incidence of △mtDNA4977 in GC cell lines (10/13, 76.9%), GC tissues (86/108, 79.6%), matched normal tissues (73/108, 67.6%), and normal gastric mucosa of non-cancer patients (29/56, 51.8%). A significantly higher incidence of mutated △mtDNA4977 was observed in GC tissues with respect to the adjacent normal tissues (79.6% vs 67.6%, P=0.045), and they were both higher than that in normal controls (P <0.05). Most importantly, we linked the △mtDNA4977 mutations with the expression level of MnSOD and ROS contents. The cell lines containing lower expression level of MnSOD was found to have generally higher frequent △mtDNA4977 and more ROS.Conclusion The decreased anti-oxidative ability, which leads to increased ROS contents, is correlated with the mtDNA damage during gastric carcinogenesis.