Patients with systemic lupus erythematosus (SLE) have an increased risk of fracture. We used high resolution peripheral quantitative computed tomography (HR-pQCT) to measure bone geometry, volumetric bone mineral density (vBMD), cortical and trabecular microarchitecture and estimated bone strength by finite element analysis (FEA) at the distal radius and tibia to assess bone characteristics beyond BMD that may contribute to the increased risk of fracture. Thirty-three Caucasian women with SLE (median age 48, range 21-64 years) and 99 controls (median age 45, range 21-64 years) were studied. Groups were comparable in radius regarding geometry and vBMD, but SLE patients had lower trabecular number (-7 %, p < 0.05), higher trabecular separation (13 %, p < 0.05) and lower FEA-estimated failure load compared to controls (-10 %, p < 0.05). In tibia, SLE patients had lower total vBMD (-11 %, p < 0.01), cortical area (-14 %, p < 0.001) and cortical thickness (-16 %, p < 0.001) and higher trabecular area (8 %, p < 0.05). In subgroup analyses of the premenopausal participants (SLE n = 21, controls n = 63), SLE patients had significantly lower trabecular bone volume fraction [(BV/TV); -17 %, p < 0.01], trabecular number (-9 %, p < 0.01), trabecular thickness (-9 %, p < 0.05) and higher trabecular separation (13 %, p < 0.01) and trabecular network inhomogeneity (14 %, p < 0.05) in radius along with lower BV/TV (-15 %, p < 0.01) and higher trabecular separation (11 %, p < 0.05) in tibia. FEA-estimated bone strength was lower in both radius (-11 %, p < 0.01) and tibia (-10 %, p < 0.05). In conclusion, Caucasian women with SLE compared to controls had fewer and more widely separated trabeculae and lower estimated bone strength in radius and lower total vBMD, cortical area and thickness in tibia.