Capillary vessel wall thickening may contribute to the muscle fibre atrophy and impaired pulmonary gas transfer notable in SLE/MCTD. Using electron microscopy we measured the thickness of unilaminar capillary basement membranes (CBM) and quantified basement membrane laminae and pericyte layers in the skeletal muscle biopsies of 31 patients with SLE, including 14 with MCTD, and 11 controls. Capillary basement membrane thickness was significantly increased in SLE compared with controls (P < 0.01) and was significantly associated with the level of C3dg (P < 0.01). Patients with MCTD had significantly greater layering of pericytes and laminae compared with patients with SLE alone (P < 0.0001 for both variables). Multiple stepwise regression analysis indicated that ANA titre was a good predictor of pericyte layering (R = 0.63, P = 0.003) and of basement membrane lamination (P < 0.0001), with steroid therapy having a significant negative association with the number of laminae (P < 0.02). A negative association between KCO and the number of layers of basement membrane (R = 0.51, P = 0.01) was documented. However, multiple regression analysis revealed no association between parameters of thickened vessel walls and the presence of muscle fibre atrophy.