The purpose of this study was to analyze the effect of orthodontic treatment with removable appliances on the growth of Candida spp. in children undergoing orthodontic treatment. The study included 60 patients of equal numbers as to gender from the orthodontics department of the Pomeranian Medical University in Szczecin, Poland. All patients were aged 6–12 years and were qualified for orthodontic treatment with removable appliances. The following examinations were performed on the day of treatment initiation (T1) and 6 months after the start of treatment (T2); a collection of oral swabs for culture on Sabouraud’s medium and the identification of fungal colonies using the VITEK®2 YST. At T1, 42 (70%) subjects, were free of Candida, while after 6 months of treatment, the number decreased to 25 (41.67%). Two types of fungi, C. albicans and C. parapsilosis, predominated in the test performed at T1. The study at T2 showed that C. albicans most frequently colonized the oral cavity in 23 children (38.33%). Three new strains C. dubliniensis, C. kefyr, and C. krusei were identified at T2. Statistical analysis showed a significant correlation between the culture results and the age of the patient at T2. Patients older than 9 years had significantly more positive tests. Orthodontic treatment with removable appliances contributes to increased oral colonization by Candida spp.