Intrauterine transmission of HHV-6 is well established in immunocompetent women while few data are available on infections in babies born to HIV-positive mothers. To assess the rate of HHV-6 vertical transmission in comparison to CMV, we analyzed cord blood spots dried on cards (Dried Blood Spots, DBS) collected during a multi-center study on HIV congenital infections in Italy. DBS were tested by PCR for HHV-6 and CMV footprints. HHV-6 amplimers were sequenced and characterized. As control group, cards taken from babies born to HIV-negative mothers were analyzed. DBS of 187 babies born to HIV-positive and 372 to HIV-negative mothers were analyzed. The prevalence of HHV-6 was 3.2% in babies born to HIV-positive mothers. CMV was found in the HIV-positive group with a prevalence rate of 1.6%. In newborns of control pregnant women, HHV-6 prevalence rate was 1.1% (p=0.09), while CMV was not detected (p=0.04). Sequence analysis could distinguish between HHV-6 A and B variant in both groups and one A/B coinfection was found in a baby born to a HIV-positive mother. HIV-infected mothers transmit HHV-6 and CMV viruses to their babies more frequently than uninfected women.