Most adults with regular transposition (the combinations of concordant atrioventricular and discordant ventriculo-arterial connections) have undergone either the Mustard or Senning procedure in childhood. It is unclear whether adverse events differ according to the surgery performed. With this in mind, we conducted a systematic review and meta-analysis to compare long-term outcomes. We searched systematically entries to MEDLINE and EMBASE databases from January 1966 through August 2003, supplementing the search by secondary sources. Comparative studies were required to include at least 10 patients in each cohort of Mustard or Senning procedure, and to report overall survival. Data were extracted by two independent reviewers. We used a component approach to assess quality. On the basis of assessment of heterogeneity, we then used a random-effects model for pooled analyses. In all, we included seven studies, incorporating 885 patients. We found a trend towards lower mortality for the 369 patients undergoing a Mustard procedure when compared to 474 submitted to the Senning operation, with a hazard ratio of 0.63 and 95% confidence intervals between 0.35 and 1.14 (p = 0.13). This trend increased with the size of the sample (p = 0.004). Obstruction in the systemic venous pathway was more common in those having the Mustard procedure, with a risk ratio of 3.5 and 95% confidence intervals from 1.8 to 7.0 (p < 0.001), with a trend towards greater obstruction of the pulmonary venous pathway in those undergoing the Senning procedure, 7.6% vs. 3.8% (p = 0.27). A trend towards fewer residual shunts was observed for those with Mustard baffles, 7.0% vs. 14.1% (p = 0.10). Sinus nodal dysfunction, however, was more common after the Mustard procedure. Data regarding atrial tachydysrhythmias was inconclusive. Systemic cardiac failure and functional capacity, was similar. We conclude that outcomes are not uniform among patients submitted to the Mustard and Senning procedures. Knowledge of such differences may facilitate stratification of risk and follow-up.