This report describes the case of a boy with prolidase deficiency who presented with splenomegaly and leg ulcers. Laboratory examination revealed hypergammaglobulinaemia, hyperimmunoglobulinaemia E, increased erythrocyte sedimentation rate, elevated transaminases, positive antinuclear and anti-double-stranded DNA antibodies, and complement consumption. No haematological, renal or articular problems were detected; neutrophil count was normal. The skin lesions were thought to be of vasculitic origin, and a diagnosis of systemic lupus erythematosus was made although the requirements for diagnosis of systemic lupus erythematosus based on American Rheumatism Association criteria were not satisfied. The child was treated with immunosuppressive drugs with worsening of skin lesions before the diagnosis of prolidase deficiency. Prolidase deficiency and systemic lupus erythematosus share a number of common immunological features and at least three patients with prolidase deficiency and immunological and clinical findings fulfilling the diagnostic criteria for systemic lupus erythematosus of the American Rheumatism Association are reported in the literature. Here we review pathogenetic hypothesis linking the metabolic defect to the disturbance in immune function. In particular we discuss the role of highly increased rates of apoptosis and/or abnormal processing of apoptotic keratinocytes in prolidase deficiency and the role of C1q deficiency, which is associated with the failure of normal clearance of apoptotic cells bearing on their surfaces many of the autoantigens involved in systemic lupus erythematosus.