Objective To evaluate informal physician judgement versus pretest probability scores in estimating risk in patients with suspected coronary artery disease (CAD). Methods We included 4533 patients from the PROMISE (Prospective Multicenter Imaging Study for Evaluation of Chest Pain) trial. Physicians categorised a priori the pretest probability of obstructive CAD (≥70% or ≥50% left main); Diamond-Forrester (D-F) and European Society of Cardiology (ESC) pretest probability estimates were calculated. Agreement was calculated using the κ statistic; logistic regression evaluated estimates of pretest CAD probability and actual CAD (as determined by CT coronary angiography), and clinical outcomes were modelled using Cox proportional hazard models. Results Physician estimates agreed poorly with D-F (κ 0.16; 95% CI 0.14 to 0.18) and ESC (κ 0.04; 95% CI 0.02 to 0.05). Actual obstructive CAD was significantly more prevalent in both the high-likelihood (OR 3.30; 95% CI 2.30 to 4.74) and the intermediate-likelihood (OR 1.43; 95% CI 1.16 to 1.76) physician-estimated groups versus the low-likelihood group; ESC similarly differentiated between the three groups (OR 9.07; 95% CI 2.87 to 28.70; and OR 3.87; 95% CI 1.22 to 12.28). However, using D-F, only the high-probability group differed (OR 2.49; 95% CI 1.74 to 3.54). Only physician estimates were associated with a higher incidence of adjusted death/myocardial infarction/unstable angina hospitalisation in the high-probability versus low-probability group (HR 2.68; 95% CI 1.52 to 4.74); neither pretest probability score provided prognostic information. Conclusions Compared with D-F and ESC estimates, physician judgement more accurately identified obstructive CAD and worse patient outcomes. Integrating physician judgement may improve risk prediction for patients with stable chest pain. Trial registration number NCT01174550 .