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Abstract Background Conventional brackets are often used during orthodontic therapy of patients with malocclusion. The complex construction of such brackets greatly inhibits oral hygiene, which predisposes to increased carriage of microbiota. Orthodontic brackets could act as reservoir of yeast and predispose to oral candidosis. The aim of this study was to assess Candida prevalence and the role of oral hygiene during fixed appliance therapy. A further aim was to characterize the isolated yeasts according to their ability to form biofilms. Methods Seventeen participants (average age 17 ± 7 years) were monitored by taking oral rinses and elastomeric ligature samples, and by evaluating the approximal plaque index (API) and gingival bleeding index (GBI) before and after placement of the orthodontic conventional brackets for 12 weeks. Isolated yeasts were counted and biofilm formation was evaluated. Results One hundred and sixteen samples (67 oral rinses and 49 orthodontic elastomers) were collected. Ten patients (58.8% subjects) were Candida-carriers (two were colonized after bracket placement) and C. albicans was the most common species. The average number of yeasts in the oral cavity showed some fluctuation during the study, but in general had an upward trend (adj. R2 = 0.7967, p = 0.07025). A correlation was found between median number of yeasts and the periodontal indices (API, GBI). The average API values decreased in the Candida-carriers (adj. R 2 = 0.95; p = 0.01709), while average GBI values increased in the noncarriers (adj. R 2 = 0.92; p = 0.0256). Conclusions Treatment with orthodontic appliances promotes Candida yeast colonization, which is variable over time in terms of strain and species, with dominance of C. albicans, and without increased biofilm-forming activity. The API value decreases over time in carriers, and the GBI value increases in uncolonized patients, which may have predictive significance for the development of oral candidiasis during orthodontic treatment.