The aim of this randomized controlled trial was to evaluate the effects of 18 months of calisthenics and endurance training regimens on bone mineral density (BMD) in perimenopausal women. Clinically healthy sedentary female volunteers (n = 105) aged 52–53 years were randomly assigned to a calisthenics (n = 36), endurance (n = 34), or control (n = 35) group. The calisthenics training (2.6 times per week on average, 50 minutes per session) consisted of rhythmic strength-endurance exercises by large muscle groups, and the endurance training (3.2 times per week, 50 minutes) consisted of walking, stair climbing, ergometer cycling, and jogging at a controlled heart rate zone corresponding to 55–75% of the individual maximal oxygen uptake (VO2max) of the subjects. The control subjects performed a light stretching program once a week. The BMD of the lumbar spine (L2-L4), right femoral neck, calcaneus, and distal radius was measured by dual-energy X-ray absorptiometry at 0, 4, 8, 10, 14, and 18 months, and the maximal isometric strength during trunk extension and flexion, leg extension, and arm flexion and the VO2max by ergospirometry were evaluated at 0, 8, 10, and 18 months of intervention. The VO2max improved significantly (p = 0.021) in the endurance group. The linear trend of the femoral neck BMD in the endurance group, as determined by generalized linear models, was significantly different (p = 0.043) from that of the control group, the trend indicating a maintenance of the prestudy BMD. In the calisthenics group, the training effect was not significant. However, the distal radius BMD of the endurance group showed a significant negative trend (p = 0.006). These results suggest that multiexercise endurance training maintains the BMD the clinically important femoral neck of perimenopausal women. This form of endurance training proved also to be feasible for healthy perimenopausal women.