The introduction of non-B HIV-1 variants into Western Europe and North America is of great concern since diagnostic tools and drugs are mainly optimised for targeting HIV-1 subtype B viruses. Madrid is an endemic area for HIV, and either the final destination or transient location for many immigrants from HIV-1 non-B endemic areas (mainly from Africa and South America). From a total of 902 HIV seropositive individuals examined since June 1999, only 27 (3%) were found to be infected with non-B HIV variants. However, up to 71.4% of African immigrants carried non-B viruses. Therefore, HIV subtyping should be requested from all HIV infected African immigrants before considering viral load testing and recommending antiretroviral therapy.