The aim of this study was to assess quantitative and qualitative alterations in the carrier rate of Candida spp. in south-eastern Turkey among adolescents, and to investigate the effect of fixed orthodontic appliances on the Candida count in a 1-year follow-up study. In the first phase of the study, the oral Candida carriage rate of 72 patients was evaluated. Samples were collected from the dorsal surface of the tongue, the mid-palate and saliva. In the second phase of the study, 42 patients who were determined to be carriers of oral Candida were treated with fixed orthodontic appliances, and from these patients a second set of samples were collected from the saliva and the orthodontic brace surfaces of eight teeth adjacent to the enamel surfaces. The saliva samples were collected before and during orthodontic treatment at 1st, 6th and 12th month, and samples from the braces were collected during the 1st, 6th and 12th month of treatment. Forty-two of the 72 patients (58.5%) were oral Candida carriers. The distribution of Candida spp. in these patients was as follows: (i) Candida albicans was identified in 31 patients (73.8%), (ii) C. tropicalis, C. krusei and C. kefyr were found in three patients each (7.14%) and (iii) C. parapsilosis occurred in two patients (4.76%). During orthodontic treatment, the micro-organism count increased both in the saliva and on tooth surfaces. The results indicate that the prevalence of oral Candida spp. is high in young adults in south-eastern Turkey and that the Candida counts increase when braces are involved.