By conventional 2-dimensional histomorphometric analysis, we have shown that cancellous bone architecture is markedly altered in hypoparathyroidism. We have now extended these observations to a 3-dimensional analysis using microcomputed tomography. Percutaneous iliac crest bone biopsies were analyzed by high-resolution microcomputed tomography from the following 25 subjects with hypoparathyroidism:​ 5 postmenopausal women, 13 premenopausal women and 7 men. Thirteen living premenopausal healthy controls and 12 cadaver subjects without bone disease served as matched controls. Hypoparathyroid subjects had significantly greater bone surface density (BS/TV:​ 5.74 ± 4.7 vs. 3.73 ± 1.01 mm²/mm³ [mean ± SD];​ p = 0.04), trabecular thickness (Tb.Th:​ 0.25 ± 0.19 vs. 0.17 ± 0.04 mm;​ p = 0.04), trabecular number (Tb.N:​ 2.99 ± 3.4 vs. 1.62 ± 0.39 mm⁻¹;​ p = 0.05) and connectivity density (Conn.D:​ 16.63 ± 18.7 vs. 8.39 ± 5.8 mm³;​ p = 0.04) in comparison to matched controls. When an additional 8 hypoparathyroid (total n = 33) and 24 cadaver (total cadaver n = 36) subjects were added to the groups for an unmatched analysis, hypoparathyroid subjects had significantly greater cancellous bone volume (BV/TV:​ 26.98 ± 10 vs. 15.39 ± 4%;​ p < 0.001), while trabecular separation (Tb.Sp:​ 0.642 ± 0.10 vs. 0.781 ± 0.13 mm;​ p < 0.001) and estimation of the plate-rod characteristic (SMI:​ − 0.457 ± 1.52 vs. 0.742 ± 0.51;​ p < 0.001) were significantly lower, the latter observation implying a more plate-like trabecular structure. Variables of cancellous bone structure in the hypoparathyroid subjects, as assessed by microcomputed tomography, were highly correlated with those assessed by conventional histomorphometry. We conclude that cancellous bone in hypoparathyroidism is abnormal, suggesting that parathyroid hormone is required to maintain normal trabecular structure. The effect of these structural changes on bone strength remains to be determined.