This descriptive, cross-sectional study was carried out to explore the frequency of contamination with TORCH agents in neonates with congenital malformations in a referral centre in Gorgan city, Islamic Republic of Iran. Blood samples were taken from 64 neonates and their mothers over a 20-month period in 2003–04. Serologic tests showed that 4/64 infants born with congenital malformations (6%) had positive IgM antibody titres for Toxoplasma gondii (2 cases), rubella virus (1 case) and cytomegalovirus (1 case). IgM was positive in 9/63 mothers (14%), also for T. gondii (3 cases), rubella virus (3 cases) and cytomegalovirus (3 cases). No cases of herpes simplex virus type II or Treponema pallidum were found.