Microsporidiosis is recognized as an increasingly important infection, particularly in patients with human immunodeficiency virus (HIV) infection. In this retrospective study we have reviewed the clinical features, laboratory findings and management of 42 HIV positive patients co-infected with microsporidia. All patients had spores identified in faeces stained with a modified trichome blue stain. Patients were all markedly immunosuppressed (median CD4 20 cells/μl). Common symptoms included weight loss, diarrhoea, abdominal pain, anorexia and nausea. 29 patients were diagnosed with Enterocytozoon bieneusi infection; 13 were infected with Encephalitozoon intestinalis, and disseminated disease was confirmed in 8. Albendazole therapy in patients with E. intestinalis (but not E. bieneusi) resulted in good clinical response.