Orthodontic appliances modify the local environment of the oral cavity, increase the accumulation of dental plaque, and affect the condition of the gingiva. The aim of this study is assessment of Brazilian propolis toothpaste's effect on plaque index (PLI) and gingival index (GI) in patients with CL/CLP treated using orthodontic appliances in the 35-day study period. The study population included 96 patients of an Orthodontic Outpatient Clinic, ACSiMS in Bytom. All the patients participated in the active phase of orthodontic treatment using buccal multibracket appliances or removable appliances. During the first examination, each patient was randomly qualified to the propolis group or control group. A statistically significant decrease in GI and PLI in the entire propolis group (P < 0.01) was shown during repeated examination. Insignificant change in GI was in the entire control group during the repeated examination compared to the baseline. Similar result was obtained in patients treated with multibracket and removable appliances. The orthodontic appliance type did not affect the final dental plaque amount and gingival condition in patients using the propolis toothpaste. These results may be clinically useful to improve prevention and control oral infectious diseases during orthodontic treatment patients with oral cleft.