The number of nosocomial bloodstream infections due to Candida species in critically ill newborns is increasing. This pathogen may be vertically transmitted from the mother or nosocomially acquired in the nursery. The goal of this study was to identify the route of transmission of unique Candida species and strains from mothers to their preterm offspring. Specimens from mothers for fungal cultures were obtained before delivery, and specimens from infants for sequential fungal cultures were obtained at defined intervals. Candida species were identified by standard methods and were typed by electrophoretic karyotyping (EK) and restriction endonuclease analysis of genomic DNA (REAG) with pulsed-field gel electrophoresis. Antifungal susceptibility testing was performed on all isolates. Fungal cultures were positive for Candida species in 12 (63%) of 19 mothers' specimens and in seven (33%) of 21 infants' specimens. EK and REAG revealed that both the mother and the infant in three (14%) of 21 mother-infant pairs were colonized with the identical strain of Candida albicans. C. albicans was most commonly transmitted vertically. Candida parapsilosis colonized other infants and could not be accounted for by a maternal reservoir.