We applied confocal laser scanning microscopy to fluorescence overlay antigen mapping (FOAM) for differential diagnosis of bullous pemphigoid (BP) and epidermolysis bullosa acquisita (EBA). FOAM of tissue-bound IgG and marker basement membrane components (BMCs) including integrin beta 4, laminin-1, laminin-5 and type IV collagen, showed that tissue-bound IgG in perilesional skin samples from five patients with BP was localized on the epidermal side of type IV collagen, and colocalized with some of the other three BMCs, whereas IgG in a sample from a patient with EBA was on the dermal side of all the BMCs. FOAM of binding sites of autoantibodies in patients' sera and markers including integrin beta 4, laminin-1, type IV collagen and type VII collagen, showed that the binding sites of autoantibodies from 16 patients with BP were localized on the epidermal side of type IV and type VII collagens, and localized above or codistributed with integrin beta 4 and laminin-1, whereas those from five patients with EBA were codistributed with type IV and type VII collagens, and localized on the dermal side of integrin beta 4 and laminin-1. These spatial relationships are compatible with their previously described ultrastructural locations. Thus, this method appears to be useful in the differential diagnosis of BP and EBA.