OBJECTIVE: Surgeons have been criticised for not undertaking high-quality research. This study examines the quality of randomised controlled trials (RCTs) in the cardiothoracic surgical literature with a view to revisiting the role of RCTs in surgical research. METHODS: All RCTs published in 1998 and 1999 in three major international cardiothoracic journals were analysed for basic components of trial design and presentation. RESULTS: We found 119 papers presented as RCTs. The median size of treatment arms per RCT was 20 (interquartile range 14-40). Of 20 dimensions of trial quality examined, 12 or more were deficient (not described or performed inadequately) in half of the studies. Key information was frequently missing. Additionally, most trials relied on 'soft' endpoints, using surrogate (72, 61%) rather than clinical, and numerical (102, 86%) rather than categorical outcomes suggesting lack of power to detect clinically relevant differences. Although most trials reported positive results (73, 63%), only in 18 (15%) did authors make recommendations for practice change. CONCLUSIONS: Many RCTs in surgery by virtue of their design, sample size, and insufficient power are incapable of answering the questions researchers seek to address. Surgical trials often may not exclude bias because of lack of blinding and variations in surgical technique and performance. It is arguable that for most study questions in clinical surgery, comparative analysis of large case series and databases will provide more robust evidence.