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Background: To describe the epidemiology of HIV and AIDS by geographical origin in the EU,1999–2006. Methods: AIDS and HIV cases from the EU 27, Norway and Iceland reported to European Centre for Epidemiological Monitoring of AIDS were analysed. Results: Of 75 021 AIDS reports over 1999–2006, 35% were migrants. Of 2988 heterosexual AIDS reports in 2006, 50% were migrants, largely from Sub-Saharan Africa (SSA), 20% of 1404 AIDS cases in men who have sex with men (MSM) were migrants from Latin-America and Western Europe. Of 57 mother-to-child transmission (MTCT) AIDS cases, 23% were from SSA. AIDS cases decreased from 1999 to 2006 in natives (42%), Western Europeans (40%) and North Africa and Middle East (34%), but increased in people from SSA (by 89%), Eastern Europe (by 200%) and Latin-America (50%). Of 17 646 HIV infections in men and 9066 in females in 2006, 49 and 76% were migrants, largely from SSA. Of 169 MTCT infections, 41% were from SSA. Conclusion: Migrants, largely from SSA, represent a considerable proportion of AIDS and HIV reports in EU, especially among heterosexual and MTCT infections. Their contribution is higher among female reports. A substantial percentage of diagnoses in MSM are migrants, largely from Western Europe and Latin-America. [ABSTRACT FROM AUTHOR]