Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) account for millions of cases of vertical infections worldwide. Laboratory diagnosis is essential for the detection of potentially infectious carriers. HBeAg represents the best serological marker for HBV replication. Since 10% of HBeAg-negative carriers transmit the virus to their children, determination of viral DNA is more reliable for the assessment of the risk to vertical infection. Risk assessment of vertical HIV transmission and monitoring AZT therapy during pregnancy are achieved by determination of HIV-1 viral load and CD4+ cell count. HIV-1 RNA or cDNA detection permits a nearly 100% sensitive diagnosis of congenital HIV infection already 2 weeks after birth. While qualitative HBV DNA determination should be limited only to anti-HBe carriers in order to assess infectiosity, HIV-1 RNA measurement represents in combination with the CD4+ cell count the best prognostic marker for vertical HIV infection and for the follow-up of infected children.