To analyse the relatedness of colonizing candidal isolates from very-low-birthweight infants hospitalized in a neonatal intensive care unit (NICU), we prospectively collected 86 candidal isolates from 20 infants, including 67 isolates of Candida albicans from 15 infants, 17 isolates of Candida parapsilosis from five infants and two isolates of Candida glabrata from one infant, who also had C. albicans colonization, over a one-year period. All 86 isolates were genotyped by infrequent-restriction-site polymerase chain reaction (IRS-PCR) and electrophoretic karyotyping (EK) with pulsed-field gel electrophoresis. A total of 15 genotypes were identified by IRS-PCR and 12 genotypes by EK. Some infants shared a common genotype. From a single infant, an identical genotype was found in 11 of 13 cases where at least two isolates of same Candida species were available for genotyping analysis, regardless of anatomical site, how many isolates were recovered or how many times. Should an infant harbour a candidal strain, they may harbour this strain at multiple sites and for a prolonged period.