Synchronous cancer of the stomach and rectum is very rare. In a special population of pilots, especially fighter pilots, synchronous rectal and gastric cancer is much more uncommon. We herein report a case of synchronous carcinoma of the rectum and stomach. The patient was a 44-year-old male fighter pilot who complained with bloody stool and altered bowel habits. He was diagnosed with hereditary nonpolyposis colorectal cancer with a definite family history, and subsequently he underwent simultaneous low anterior resection and distal gastrectomy with D2 lymphadenectomy. Postoperative pathologic assessment showed a poorly differentiated gastric adenocarcinoma with signet ring cell components (pT2N1M0; stage IIb) and a moderately differentiated rectal adenocarcinoma with myxoid components (pT3N0M0; stage IIa). Both tumors showed positive expression of p53, Ki-67, VEGF, carcinoembryonic antigen, MRP, TS, P-gp, and TopoII, and negative expression of c-erbB2, CD34, CD31, D2-40, S-100, FVIII, MLH1, MSH2, and MSH6 oncoproteins. Six cycles of XELOX chemotherapy and 50 Gy/25 f radiotherapy were delivered postoperatively. Now, he has returned to his work under medical observation for about 6 months. From this patient’s diagnosis and treatment, we think that the gene screening should be used in pilot selection. According to the result of gene screening, we can give pertinence examinations to the target organ of genes. It is very necessary for pilots to keep keen vigilance at gastrointestinal tumors because they have to face many high-risk factors in working. As to pilots, the selection of operation should be individualized.