Purpose The present meta-analysis aimed to compare the diagnostic accuracy of more recent computed tomography coronary angiography (CTCA) with invasive coronary angiography (ICA) in the assessment of graft patency after coronary artery bypass graft surgery (CABG). Material and methods A systematic review was performed using nine electronic databases from their dates of inception to July 2015. Predefined inclusion criteria included studies reporting on comparative outcomes using ≥ 64 slice multidetector computed tomography (MDCT) and ICA. The primary endpoints included graft occlusion and significant graft stenosis ≥ 50%. Secondary analyses included the comparison of arterial versus venous graft conduits, and the use of different MDCT techniques. Results Thirty-one studies were identified according to selection criteria, involving 1975 patients with 5364 assessed grafts. Combined assessment of stenosis and occlusion for all grafts demonstrated a sensitivity of 96.1% [95% confidence interval (CI) 94.3–97.4%] and specificity of 96.3% (95% CI 95.1–97.3%). CTCA assessment of venous grafts demonstrated higher sensitivity compared to arterial grafts, when testing for both occlusion and stenosis (97.6% vs 89.2%, p = 0.004). Conclusion Results of this study demonstrated that CTCA had a relatively high pooled sensitivity, specificity and negative predictive value compared to ICA. However, patient baseline characteristics varied between studies, and the results should be interpreted with caution. Nonetheless, our results indicate that CTCA should be recognized as an accurate and non-invasive investigation for graft patency in symptomatic patients after CABG.