Candida albicans is a fungal pathogen, but also a commensal in many individuals. Since detailed molecular studies of children carrying C. albicans are lacking, we longitudinally investigated fecal and tonsillopharyngeal samples from 10 children undergoing treatment for cancer, six children treated for cystic fibrosis (CF), and seven healthy children during the time period of 1999-2008. Multilocus sequence typing (MLST) was performed on 62 C. albicans isolates. Only three of the 23 children (13%) were colonized with genetically unrelated strains in the longitudinal follow-up. We identified 32 different diploid sequence types (DSTs), but only one (409) was shared by two siblings. Most often, the fecal strain types were identical or closely related to the tonsillopharyngeal reservoirs. We found no closely related strain types in children who were hospitalized in the same ward or in children attending the same day care center. There was no sign of resistance to fluconazole, caspofungin, amphotericin B or flucytosine over time. This study shows that both children with cancer or CF, and healthy children usually harbor the same C. albicans strain over time. We did not find indications of clonal spread between children in the same environments, except in a pair of siblings.