Background: To investigate relationship of the Nin one binding protein (NOB1) gene with the prognosis of gastric cancer (GC). Methods: The GC tumor tissues and paired adjacent normal gastric tissues were collected from 65 patients who underwent primary gastric resection surgery in our hospital from January 2009 to July 2011. Data including age, gender, family cancer history, tumor diameter, pathological type, differentiation, clinical stage by tumor node metastasis (TNM) staging, lymphatic metastasis, and distant metastasis were collected. Expression of NOB1 and VEGF was determined using real time PCR. The relationship of NOB1 with clinical outcomes and prognosis of GC patients was analyzed by statistical methods. Results: Both mRNA expression of NOB1 and VEGF was significantly higher in tumor tissues than that of the normal tissues, p < 0.05, and mRNA expression of NOB1 was positively correlated with mRNA expression of VEGF by Pearson's correlation analysis. Significant difference was observed in TNM stage, tumor differentiation, and metastasis between the low and high NOB1 expression groups, p < 0.05, while no significant difference was observed in age, gender, family cancer history, tumor location, and diameter. Univariate analysis showed that TNM stage, tumor differentiation, lymphatic metastasis, distant metastasis and expression of NOB1 and VEGF were all significantly different in survival and dead patients. Logistic analysis showed that NOB1 was an independent risk factor for 5-year mortality of GC patients, as well as lymphatic metastasis and distant metastasis. Conclusions: NOB1 was correlated with clinical outcomes and prognosis of GC patients and was an independent risk factor for 5-year mortality of GC patients. This study might provide more clinical evidences for NOB1 in GC and give a new target for diagnosis and treatment for GC patients.