Background Myocardial single-photon emission computed tomography (SPECT) has high prognostic value for cardiac events. Coronary computed tomographic angiography (CCTA) provides information on coronary stenosis severity with excellent diagnostic accuracy. The aim of this study was to investigate the prognostic value of myocardial perfusion abnormality on SPECT in relation to the severity of coronary artery stenosis on CCTA in patients with suspected with coronary artery disease (CAD). Methods Between November 2004 and November 2011, a total of 1286 patients with suspected CAD (63.3% male and 62.1짹10.4 years) undergoing both SPECT and 64-slice CCTA (within 3 months) were enrolled from two centers. Fixed and reversible perfusion defect on SPECT were considered as abnormal myocardial perfusion imaging (MPI). In CCTA, maximal coronary luminal narrowing ( >2 mm in diameter) was graded as <25%, 25~49%, 50~69%, 70~89%, or ���90% visual diameter reduction. The cardiac events including all-cause death, non-fatal myocardial infarction, unstable angina and revascularization (>90 days after the exam) were obtained from the medical records or telephone interview. Event rates were analyzed according to the test results. Results Four hundred and eighty-six (37.8%), 235 (18.3%), 291 (22.6%), 156 (12.1%) and 117 (9.1%) patients had stenosis of <25%, 25~49%, 50~69%, 70~89%, or ���90% on CCTA, respectively, and 408 (31.7%) had abnormal MPI on SPECT. During the follow-up (median 738 days), 160 (12.4%) patients suffered cardiovascular events (61 all-cause death, 11 myocardial infarction, 75 unstable angina, and 19 revascularization). After adjustment for baseline characteristics in a multivariate model, both CCTA stenosis ���50% (n = 563, 43.7%) (OR 2.35; 95% CI: 1.61-3.43; P <0.001) and abnormal MPI (OR 2.98; 95% CI: 2.12-4.18; P <0.001) were independent predictors for events. However, when the subgroup analyses by the stenosis severity on CCTA were performed, abnormal MPI was not a predictor for future cardiovascular events in the groups with stenosis of <25% or >90% on CCTA (P >0.05), whereas abnormal MPI remained a significant predictor of events in the groups of 25~90% stenosis on CCTA (P <0.05). SPECT provided incremental prognostic values particularly in the groups with stenosis between 25% and 90% (P >0.05) but not in the groups with stenosis of <25% or >90% on CCTA (P <0.05). Conclusion In patients with suspected CAD, SPECT has limited prognostic value in patients with mild (<25%) or severe (>90%) coronary artery stenosis on CCTA, whereas SPECT provides incremental prognostic values especially in patients with stenosis between 25% and 90% on CCTA.