Phosphorus and calcium are essential for bone health. There is a concern that a low calcium/phosphorus intake ratio resulting from low calcium intake coupled with high phosphorus intake may have a negative effect on bone mineral status, especially in Western countries. The objective of this study was to examine cross-sectionally the influence of habitual phosphorus and calcium intake and the calcium/phosphorus intake ratio on the bone mineral density (BMD) in 441 young Japanese women (aged 18-22) whose calcium/phosphorus intake ratio was assumed to be lower than young Western women. We also ascertained the relationship between dietary intake and serum or urinary measurements of phosphorus and calcium. Parathyroid hormone (PTH) and 25-hydroxy vitamin D (25(OH)D) were also examined for 214 of the 441 subjects. Phosphorus and calcium intake and the calcium/phosphorus intake ratio had significant positive correlations with urinary phosphorus. Calcium intake and the calcium/phosphorus intake ratio independently had positive and significant associations with BMD in the distal radius adjusted for postmenarcheal age, body mass index, and physical activity. There were no significant associations with BMD in the lumbar spine and femoral neck. These results indicate that in young Japanese women, phosphorus intake did not have a significantly negative effect on bone mineral density, and calcium intake and calcium/phosphorus intake ratio had a small but significant association only in a site-specific manner with BMD.