We studied the effect of different training patterns on vertebral trabecular and cortical bone mineral density (BMD) in male athletes using quantitative computed tomography. Vertebral trabecular (t) and cortical (c) BMDs of the first three lumbar vertebrae were measured using single energy quantitative computed tomography in 51 athletes including 10 weight lifters (mean age 20 years), 13 soccer players (mean age 27 years), 28 wrestlers (mean age 17 years), and 45 age-matched volunteers (mean age 21 years). Measured BMDs were correlated with age, body height and weight, training hours per week, sports years, and type of physical activity. Vertebral tBMDs were found to be 44%, 23%, and 24% higher in the weight lifters, soccer players, and wrestlers, respectively, compared with the volunteers. The corresponding cBMDs were 18%, 6%, and 11% higher than that of volunteers. There was significant correlation between the trabecular and cBMD, and height of the athletes, sports years, training hours per week, and physical activity. The most significant correlation with BMD was the type of physical activity. Both the height of the subjects and physical activity variables showed variations of 47% and 32% in trabecular and cBMD, respectively. According to the multiple analysis of variance (MANOVA) only the physical activity factor was effective, with a significance level of P < 0.01; the other factors and interactions were not effective (P > 0.05) on trabecular and cBMD. Different training patterns have a different anabolic effect on both trabecular and cBMDs of the vertebrae, and this effect is more pronounced on the trabecular compartment. Weight lifting showed the highest anabolic effect on both trabecular and cBMDs compared with soccer playing and wrestling. Of the independent variables, physical activity showed the highest anabolic effect on the vertebrae. These results may have implications for devising exercise strategies to reduce the possibility of fracture in old age.