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In order to investigate the impact of Pneumocystis carinii infection in southern Spain following the introduction of highly active anti-retroviral therapy (HAART), all cases of pneumocystosis between 1998 and 1999 were identified from data compiled by the national surveillance system. In total, 498 cases of pneumocystosis were recorded, of which 87% involved HIV-positive patients. The mean age, length of hospital stay and mortality were higher for HIV-negative patients. There was a higher number of cases in winter. Despite HAART implementation, pneumocystosis remains a significant health problem for both HIV-positive and HIV-negative patients.