Self-etching primers (SEP) have recently simplified the orthodontic bonding process and questions have arisen regarding their reliability and efficiency. The goal of this study was to assess the importance of a pumice prophylaxis prior to bonding with SEP (Transbond Plus, 3M Unitek, Monrovia, CA) in reducing bond failures. Thirty orthodontic patients volunteered to participate in this split-mouth prospective clinical trial. A pumice prophylaxis experimental group and a non-pumice control group of teeth were randomly assigned in a contralateral quadrant pattern within each patient. A total of 508 teeth were bonded and monitored over 3 months for bond failures. There were 35 total failures (6.9%) with 6 (2.4%) in the pumice group and 29 (11.4%) in the non-pumice group. Bond failures were compared as a total number between groups and also as the number of patients who experienced bond failures with each method using Chi-square analysis. There were statistically significant differences both in the total number of bond failures (P < .001) and in the number of patients with bond failures between groups (P < .01). A significantly lower and clinically acceptable bond failure rate was demonstrated when using Transbond Plus SEP after pumice prophylaxis. This study produced strong evidence to suggest the need for pumice prophylaxis in orthodontic bonding when using SEP.