Molecular assays related to cell proliferation correlate with stage and/or survival in a variety of tumors. We immunostained formalin-fixed, paraffin-embedded tissue sections from 61 patients with gastric adenocarcinoma (21 biopsy and 40 gastrectomy specimens) for cyclin A, cyclin B1, p34cdc2, p120, MIB1, and proliferating cell nuclear antigen (PCNA) by automated methods. HER-2/neu gene amplification was analyzed by automated fluorescence in situ hybridization (FISH). Immununostains, FISH results, and pathologic stage were compared with length of survival. Forty-three percent of the cases showed amplification of HER-2/neu. Sixty-two percent of cases showed positive immunostaining for cyclin A, 38% for cyclin B1, 31% for p34cdc2, 49% for p120, 69% for MIB1, and 33% for PCNA. On univariate analysis, pathologic stage (P = .003) and HER-2/neu gene amplification (P < .001) correlated with length of survival. Cyclin A, cyclin B1, p34cdc2, p120, MIB1, and PCNA did not correlate with survival. On multivariate analysis, pathologic stage (P = .015) and HER-2/neu gene amplification (P = .002) independently predicted survival. These correlations were unrelated to tubular or signet ring cell histologic characteristics or to location within the cardia or more distally. Pathologic stage and HER-2/neu gene amplification by FISH were independent prognostic factors in gastric cancer, but the various proliferation markers that we studied did not correlate with survival.