Introduction The prevalence of HIV-1 non-B subtypes (HIV-NBS) is increasing in Europe because of emigration from countries where genetic variants are endemic. Although HIV-NBS could have a different clinical evolution and could respond differently to antiretroviral drugs than B subtypes, these variants’ response remains undocumented.

Aims We sought to determine both the prevalence of HIV-1 genetic variants and their clinical evolution in non-Spanish children infected with HIV-1.

Patients and Methods Children with HIV infection from endemic countries were tested for HIV subtypes. Twelve children less than 18 years old, born abroad or with a parent born abroad were selected.

Results Non-B subtypes were isolated in five children (42%): CRF2_AG recombinant in three cases (Equatorial Guinea), subtype C in one (Equatorial Guinea) and CRF13_cpx in the last one (India). There were neither differences in their clinical, immunological and virological evolution, nor with other Spanish children infected with HIV-1 subtype B.

Conclusions Because of the increasing frequency of patients with HIV-NBS and their unknown long-term evolution, all children from endemic countries should be tested for HIV subtypes. We believe new studies with more patients during longer times, and assessed with pharmacogenetics, could reveal differences in these patients’ clinical, immunological and virological evolution.