Mastocytosis is characterized by abnormal proliferation of mast cells especially within the skin and bone marrow and is often associated with osteoporosis. Mast cells can synthesize a variety of cytokines that are known to affect the skeletal system, but the cellular and pathophysiological mechanisms leading to osteoporosis in systemic mastocytosis remain poorly understood. To further characterize mastocytosis-associated osteoporosis we compared bone histomorphometric findings in iliac crest biopsy specimens from 158 untreated patients with mastocytosis. The overall prevalence of mastocytosis in the specimens diagnosed with osteoporosis was 1.25%, but that in patients younger than 45 years was 2.25%. The male-to-female ratio was 1:1, in contrast to 1:2 in osteoporosis. Osteopenia was present in 64% of the patients with mastocytosis, while osteosclerosis was rare (3%). Histological criteria are the concentric increase in mast cells in the perivascular tissue and the increase in elongated mast cells within the marrow space. Histomorphometry showed mastocytosis to be associated with moderate hyperosteoidosis and increased perforating bone resorption, indicated by a significant decrease in bone volume, trabecular thickness, and trabecular number as compared to controls. Osteoclast number was not altered, pointing to a functional effect of mast cells and/or its product on osteoclasts, rather than an effect on osteoclast differentiation. We conclude that although the prevalence of mastocytosis seems to be low, its correct and early diagnosis is crucial for at least 2.25% of younger patients with osteoporosis.