We report a case of a false negative diagnosis of HIV-1 infection in an African girl. Two HIV-1 DNA polymerase chain reaction (PCR) tests were negative at the second and fourth months of life. Because anti-HIV antibodies persisted when the patient was 18 months old, the HIV-1 RNA PCR test was performed with a positive result, confirming HIV-1 non-B subtype, recombinant A-G. The prevalence of non-B HIV-1 subtypes are increasing in Spain, which could be related to the phenomenon of immigration. Approximately one-third of HIV-infected foreigners have non-B subtypes and the percentage increases to 70 % of the African population in Spain. In non-B HIV-1 subtypes, false negative results and inconsistencies between viral load and CD4 count are more frequent. These subtypes also show a higher rate of resistance to protease inhibitors, which can have therapeutic implications.