Background Osteoporotic fractures are a significant cause of morbidity and mortality, particularly in developed countries. Increasing peak bone mass in young people may be the most important primary prevention strategy to reduce the risk of osteoporosis. This study aimed to examine the relationship between dietary factors and physical activity on bone mineralization in young men. Methods Thirty-five healthy men aged 18-25 y had anthropometric measures, body composition, resting metabolic rate, blood pressure, blood lipids, food intake, physical activity and cardiorespiratory fitness assessed. Results Participants who consumed more than 1000 mg/d of calcium were taller and had higher levels of whole body mineral content than participants who consumed less than 1000 mg/d of calcium. Similarly, participants who expended more than 20% of total daily energy engaged in moderate- to vigorous-intensity physical activity had higher cardiorespiratory fitness and higher levels of body mass adjusted bone mineral content than participants who did not meet this level of energy expenditure. There were no differences in blood pressure or blood lipids between participants in calcium or in physical activity energy expenditure categories. Conclusions A high intake of dietary calcium and high daily energy expenditure engaged in moderate- to vigorous-intensity physical activity were positively associated with bone mineralization in young men, particularly in the lumbar region.