It was the aim of this retrospective analysis to examine the influence of low-dose monophasic oral contraceptives (OCs) on bone mineral density (BMD) of the femoral neck and of the spine in young female endurance athletes. Data on training intensity, dietary intake, menarche, menstrual cycle disorders, years of OC use, and age at first OC use were determined by a self-report questionnaire. Only athletes performing regular endurance exercise for more than 3 years with more than 3 h of exercise per week were included in this study and underwent a clinical assessment including measurement of weight, height, spine, and hip BMD by dual-energy X-ray absorptiometry, and collection of a blood sample. The data from 75 regularly exercising endurance athletes aged 18–35 years (26.5 ± 4.8 years) were initially included in this analysis. Six athletes were later excluded due to oligo-/amenorrhea. Subjects were allocated into the OC group when they reported OC use for more than 3 years in women younger than 22 years of age, or when they reported OC use for more than 50% of the time after menarche in women aged 22–35 years. There were no differences in age, weight, height, body mass index (BMI), body fat, menarche, training intensity, age at start of training, or any serum parameters between OC users ( n = 31) and control subjects ( n = 38). However, OC users had 7.9% lower spine BMD and 8.8% lower proximal femur BMD ( P < 0.01 for both sites). When the relationship between BMD of the spine and OC use was further analyzed by a stepwise model of multiple regression analysis using OC years, age at OC initiation, BMI, and menarche as independent variables, age at first OC use was found to be the best predictor of vertebral BMD, while the only significant predictor of femoral neck BMD was BMI. We conclude that OC use is associated with decreased BMD of the spine and the femoral neck in female endurance athletes, and that early age at initiation of OC use may be an important risk factor for low peak bone mass in young women.