This clinical trial evaluated, over a 12-month period, the performance of brackets bonded to teeth etched and primed with Transbond Plus Self-Etching Primer (SEP) when compared with a conventional separate two-step etch and primer system. Thirty-nine randomly selected patients requiring fixed appliance therapy were entered into the study. Random allocation of each etching system, along with a 'split-mouth cross-quadrant' design was used. A total of 661 brackets were placed by two operators. The failure and survival rates of the brackets were determined for age and gender of the patients, each etching system, operator, mode of failure, tooth position in the dental arch, and number of manipulations prior to curing the adhesive. Statistical analysis showed that SEP had a significantly higher bond failure rate (11.2 per cent) than the conventional etch and primer system (3.9 per cent) at the P = 0.001 level. Cox's proportional hazards regression showed the conventional etch and primer system to have a 60 per cent reduced chance of bracket failure over a 12-month observation period, while males had a 2.4 times increased risk compared with females. The predominant mode of failure was at the composite enamel interface for the SEP, while for the conventional etch and primer system, it was within the composite adhesive. No statistically significant differences were found for the failure rate with respect to the age of the patient, operator, tooth location, or the number of manipulations of the bracket. This in vivo study showed that brackets bonded using SEP had an increased clinical bond failure rate compared with the conventional, separate, etch and prime system.