The aim of the study was to compare alterations of various regions of the basement membrane zone (BMZ) in lichen sclerosus (LS) using laser scanning confocal microscopy. The study included three cases of bullous LS, one case of bullous LS that developed in the course of graft-versus-host disease (GVHD), and six cases of non-bullous LS. Three cases of morphea served as a control. Biopsies from patients' skin and control biopsies from normal human skin were cut into 30-microm thick slides and labeled with antibodies against beta4-intergin (lamina lucida marker), collagen IV, and the N-terminal end of collagen VII (lamina densa markers) and the C-terminal end of collagen VII (sublamina densa marker) using routine immunofluorescence (IF). Three-dimensional (3D) reconstruction of various regions of the BMZ showed a decrease in the number and size of the dermal papillae in LS and morphea as compared with normal skin. In LS numerous invaginations and holes were present in the BMZ at the level of the lamina lucida and lamina densa. Computer animation of 3D projections revealed that the thickness of the lamina densa observed under the light microscopy is an optical artifact dependent on periodical tortion of the lamina densa along its axis. Torsions and invaginations of the BMZ are equally responsible for the phenomenon of artificial reduplication of the lamina densa observed at the ultrastructural level. IF labeling with antibody against the N-terminal end of collagen VII disclosed the presence of a large hole (up to 25 microm) in the lamina densa and the presence of granular material in deep dermis suggestive of partial degradation of lamina densa at the level of anchoring fibers. An IF mapping study showed blister formation below the lamina densa in three patients with bullous LS, whereas in a case of LS associated with GVHD, a blister formed through the basal layer of the epidermis. In morphea, there was flattening of BMZ at the level of lamina lucida, lamina densa, and sublamina densa but the continuity of BMZ was preserved. Three-dimensional reconstruction of dermal-epidermal junction in LS revealed alterations of the BMZ, most pronounced at the level of the lamina densa and sublamina densa.