The relationship of lactase malabsorption to osteoporosis is unclear. We examined the relationship of self-reported lactose intolerance (LI) to bone mineral density (BMD) in perimenopausal Finnish women. A random population sample of 2025 women aged 48-59, who underwent spinal and femoral BMD measurement with dual X-ray absorptiometry in Kuopio, Finland during 1989-1991 formed the study population. Out of these women, 162 women reported LI. The mean dairy calcium intake was 558 mg/day in women with LI and 828 mg/day in other women (p < 0.0001). The mean spinal BMDs were 1.097 and 1.129 g/cm2 (-2.8%) (p = 0.016) and the mean femoral BMDs were 0.906 and 0.932 g/cm2 (-2.8%) (p = 0.012) for the LI and other women, respectively. After adjusting for weight, age, years since menopause, and the history of hormone replacement therapy, these differences changed to -2.7% (p = 0.016) for the spinal and -2.4% (p = 0.012) for the femoral BMD, respectively. Dairy calcium intake was an independent determinant of femoral BMD. The addition of calcium intake variables into the multivariate model did not affect the spinal BMD difference, but weakened the femoral BMD difference to -1.9% (p = 0.075). Our results suggest that LI slightly reduces perimenopausal BMD, possibly through reduced calcium intake.