Gastric cancer is the second most common cancer in the world and the fifth leading cause of cancer-related death in Taiwan. To improve the survival of gastric cancer patients, biomarkers for early detection and effective anticancer therapy are required. An essential first step is to profile gene expression in gastric cancer and identify genes that are aberrantly expressed, and to do this cDNA microarrays were performed. The clinic-pathologic correlation and prognostic significance of the aberrantly expressed genes were evaluated to identify novel biomarkers of gastric cancer. Fresh surgical samples of tumour tissue and matching noncancerous mucosa were obtained immediately after gastric resection in 43 patients. Secreted Protein, Acidic and Rich in Cysteine (SPARC) (Osteonectins), one of the most highly expressed genes in both intestinal and diffuse gastric cancers in our microarray results, was selected for further study. The overexpression of SPARC was verified using real-time quantitative-reverse transcription-polymerase chain reaction (Q-RT-PCR), Northern blot and immunohistochemical staining. The expression of SPARC in tumour tissues was, on average, 4.27-fold increased (95% CI 2.68-5.85) compared to adjacent noncancerous mucosa (P<0.001). The expression of SPARC was higher in advanced (T2, T3 and T4) cancer compared to the early (T1) cancer (P=0.048) with regard to depth of wall invasion. Higher expression of SPARC was significantly associated with lymph node metastasis (P<0.001), lymphatic invasion (P=0.004) and perineural invasion (P=0.047). Expression of SPARC in patients in stage II and above was significantly higher than those in stage I (P=0.017). The 3-year survival of patients with lower expression of SPARC was significantly better than those with a higher expression (log rank P=0.047). These data indicate the potential of SPARC as a prognostic marker for gastric cancer.