This longitudinal prospective study aimed to determine the prevalence of oropharyngeal colonization by C. albicans in children with cystic fibrosis (CF), and observe the continuity of candidal colonization and the changes in production of virulence factors, susceptibility to antifungal agents and RAPD patterns of the isolates. Thirty-seven children with CF were followed-up for oropharyngeal C. albicans colonization for 18 months. The colonization rate was detected in 54%. All isolates were susceptible to amphotericin B, but those isolated from one patient were resistant to fluconazole. Biofilm production, secretory acid proteinase, phospholipase and esterase activity rates were 30%, 60%, 75% and 80%, respectively. RAPD analysis with the primers OPE-03 and OPE-18 was performed for genotyping. RAPD patterns of the strains isolated from the same patient were related to each other, whereas they were not related with other strains isolated from different patients. Two C. albicans strains isolated from the same patient were found to be unrelated to one another. As a result, long-lasting colonization of the oropharyngeal mucosa of children with CF by endogenous C. albicans isolates having the same RAPD pattern was demonstrated. Colonization prevalance and development of resistance to antifungal agents and the increased production of virulence factors were not correlated. Copyright © 2013 John Wiley & Sons, Ltd.