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Because the bone mineral density (BMD) in different anatomic regions is heterogenous the number of women who fulfill the World Health Organization definition of osteopenia or osteoporosis increases with the number of regions examined. The purpose of this study was to investigate the agreement between measurements of the spine, femur, forearm, and whole body following menopause. Two thousand and five healthy, perimenopausal women, mean age 50.6 years, were studied using Hologic QDR-1000/W and QDR-2000 densitometers. Though the BMD of different anatomic regions were correlated (r = 0.40-0.77, p < 0.01), the variability in each patient regarding T and Z scores between regions was considerable. For example, despite a high correlation (r = 0.67, p < 0.01) and no systematic difference between the T scores for total femoral and lumbar BMD, the limits of agreement (mean difference ± 2 SD) for the comparison were −1.89 to 1.87. Femoral neck T scores were 0.5 SD lower than those of the other regions, confirming reports that the young adult reference for this measurement is disproportionally high. The prevalence of osteoporosis was 1.2% when femur total BMD was considered alone and 5.9% when lumbar and ultradistal forearm results were included. However, as many as 7.9% showed osteoporosis of the femoral neck when the Hologic T score was used, compared with 0.7% using National Health and Nutrition Examination Survey (NHANES) values. The choice of anatomic region and availability of appropriate young adult reference data has considerable impact on the apparent prevalence of osteoporosis. Given the heterogeneity between regions, a combination of spinal and femoral densitometry should be used in diagnosing osteoporosis, though this increases the prevalence of osteoporosis by 50% or more in perimenopausal women.