There have been many reports of low bone mineral density (BMD) in female endurance runners. Although there have been several reports of low BMD in male runners, it is unclear how comparable the problem is to that in females. We compared BMD between male and female endurance runners and with a reference population. One hundred and nine endurance runners (65 females, 44 males) aged 19-50 years participated and had been training regularly for at least 3 years (32-187.2 km week(-1)) in events from 3 km to the marathon. BMD was measured at the lumbar spine (L2-L4) and hip by DXA. A questionnaire assessed training and menstrual status. Lumbar spine T scores were similar in male and female runners (-0.8 (0.8) versus -0.8 (0.7); f = 0.015; P = 0.904) as were total hip T scores (0.6 (7.9) versus 0.5 (9.2); f = 0.192; P = 0.662). The proportion of male runners with low lumbar spine BMD (<-1.0) (n = 16 from 44) compared to that of females (n = 27 from 65) (P = 0.675). Males had lower spine T scores than eumenorrhoeic females (-0.8 (0.7) versus -0.4 (0.7); f = 5.169; P = 0.03). There were moderate negative correlations between weekly running distance and lumbar spine BMD in males and females (r(2) = 0.267; 0.189; P < 0.001), independent of menstrual status in females (r(2) = 0.192; P < 0.001). Lumbar spine but not hip T scores were greater in runners who participated in resistance training at least twice-a-week (male: -0.4 versus -1.1; female: -0.5 versus -1.1; P < 0.01). Using multiple regression, running distance (-) and BMI (+) together best predicted lumbar spine T scores (r(2) = 0.402; P < 0.01) in females. Although weak, BMI (+) best predicted hip T scores (r(2) = 0.167; P < 0.05). In males, running distance and training years (-) together best predicted lumbar spine T scores (r(2) = 0.400; P < 0.01). Training years (-) best predicted hip T scores (r(2) = 0.361; P < 0.01). To conclude, our findings suggest that male runners face the same bone threat at the spine, as female runners. Further research in male athletes is required. Incorporation of regular resistance training into an athlete's training programme may be a useful preventative strategy.