Multi-detector computed tomography (MDCT) has high diagnostic value for detecting or excluding coronary artery stenosis. However, conventional coronary angiograms (CCA) are occasionally required in patients having persistent chest pain with normal MDCT. We retrospectively analyzed 90 patients who underwent CCA due to persistent chest pain with normal MDCT. The patients were classified into patients having more than 50% diameter stenosis in CCA (false negative, group I: n = 14, 62.6 +/- 7.5 years, 7 males) and those having less than 50% diameter stenosis (true negative, group II: n = 76, 52.1 +/- 12.0 years, 42 males). Significant stenosis was observed in 9 patients at the left anterior descending artery, 4 at the right coronary artery, and 1 at the left circumflex artery in group I. Group I patients were older than group II patients (63 +/- 8 versus 52 +/- 12 years, P < 0.001). There were more patients with hypertension and smoking in group I (64.3% versus 7.9%, 35.7% versus 3.9%, P < 0.001, P < 0.001, respectively). The levels of uric acid and homocysteine were higher in group I than in group II (5.7 +/- 1.5 versus 4.6 +/- 1.2 mg/dL, 9.6 +/- 3.1 versus 7.4 +/- 2.5 mol/L, P = 0.008, P = 0.010, respectively). There were more ST or T changes in the electrocardiograms in group I (35.7% versus 1.3%) (P < 0.001). In multivariate analysis, a history of hypertension, uric acid levels, and ischemic evidence in the electrocardiogram were independent factors for a false negative of MDCT (odds ratio 11.11, 4.76, 1.81, 95% confidence interval 4.67 to 10.00, 1.41 to 1.61, 1.05 to 3.33, P = 0.009, P = 0.012, P = 0.046, respectively). In certain situations, the findings of coronary stenosis by MDCT do not always correlate with that of CCA.