Objective To explore the association between VEGF gene polymorphism and the changes in cardiac function after HiHiLo. Methods Sixty two men of Han nationality from northern China underwent HiHiLo for 30 days. Training programme was as follows:exposure in hypoxic environment (14.8% - 14.3%O_2) 10hrs per day, hypoxic training three times per week (15.4%～14.8%O_2), and training at sea level in the remaining time. The genotype was analyzed by PCR-RFLP. Results There is an association between VEGF gene polymorphism and the changes in left ventricular structure and function after 4-week HiHiLo. LVM, LVMI, SV and SI after HiHiLo increased significantly in men carrying CC genotype were better than those carrying CT genotype. Conclusion Men of Han nationality carrying CC genotype probably have a better left ventricular function in response to the HiHiLo than those carrying CT genotype. CC genotype can be used as a genetic marker for the better responsiveness of left ventricular function to the HiHiLo.