This study compared the efficacy and efficiency of two professional prophylaxis procedures in orthodontic patients performing different oral hygiene regimens: the air powder polishing system (APP), and the rubber cup and pumice (RCP) technique. Sixty-two patients were divided into two groups: group I included 40 subjects who did not use any chlorhexidine mouthwash and group II comprised 22 subjects who regularly rinsed with a chlorhexidine mouthwash (at a 0.12 per cent concentration) and showed increased tooth staining. Using a split-mouth experimental design, the buccal and lingual tooth surfaces were cleaned in half of the mouth by the APP and in the opposite half by the RCP technique. Tooth surfaces were scored before (PRE) and after (POST) the experimental procedures for the plaque index (PI), and for the presence of tooth staining. In addition, the treatment time required by each procedure was recorded. In test group I, significant reductions in the PI after APP and RCP were observed. Likewise, in test group II, both procedures significantly reduced the baseline PI values. In both experimental groups, the percentage of stained sites significantly decreased after APP and RCP, but in test group II, APP seemed to be more effective than RCP. In addition, APP required significantly less time than RCP to remove dental plaque and staining. These data show that both professional prophylaxis procedures are effective in orthodontic patients, with APP being the most time-efficient technique and the most effective method for removal of tooth staining.