Purpose: To determine the influence of menstrual irregularity, oral contraceptive use and other factors on bone mineral density (BMD) and bone size at different skeletal sites in 135 college-aged fit women. Methods: Menstrual history, oral contraceptive use, exercise history, and nutritional factors including calcium, caffeine, and alcohol intake as well as tobacco use were determined by written survey. Height, weight and fitness levels were measured. Spine and hip BMD were measured by dual x-ray absorptiometry (DXA), calcaneus BMD by peripheral DXA, and tibial bone mineral content (BMC) and size by peripheral Quantitative Computed Tomography (pQCT). Results: The mean age was 18.4 ± 0.8 years. Weight and prior exercise were positively related to BMD at most skeletal sites and to tibial bone size. Milk intake was positively related to calcaneal BMD, tibial BMC and cortical thickness. Fracture history was an important predictor of spine, hip and heel BMD. Women who had ≥ 10 menstrual cycles in the year prior to BMD measurement had higher BMD at all sites as well as a greater tibial mineral content and cortical thickness than women who had oligomenorrhea/amenorrhea (≤ 9 cycles in the prior year; all p < 0.05). Oral Contraceptive (OC) users had significantly lower BMD in the spine (p < 0.02) and calcaneus (p = 0.04), smaller tibial periosteal circumference and lower tibial mineral content (p < 0.02) than non-OC users. Conclusion: In a population of fit, college-aged women, OC use and oligomenorrhea were associated with reduced BMD and bone size. Weight, as well as prior exercise and milk intake was positively related to bone density and size at some skeletal sites. Understanding these relationships would help improve skeletal health in young women