BACKGROUND The consequences of atherosclerosis can be detected by multislice computed tomography (MSCT), invasive coronary angiogram (CAG) and the resultant myocardial ischaemia by myocardial perfusion single photon emission computed tomography (MPS). In this study an attempt is made to compare MSCT with MPS and also to compare the MSCT findings with that of invasive CAG in patients suspected to have coronary artery disease (CAD). METHODS A total of 99 patients suspected to have CAD underwent both MSCT and MPS with (99m)Tc sestamibi. The MSCT studies were classified as having no CAD, significant CAD (>50% diameter stenosis), and insignificant CAD (<50% diameter stenosis). Myocardial perfusion single photon emission computed tomography was reported as normal and reversible ischaemia. In a subgroup of 33 patient invasive CAG was done. RESULTS In 99 patients, 396 coronaries were evaluated with MSCT and MPS. Coronary artery calcium scoring (CACS) in these patient ranged from 0 to 2200. No CAD was noted in 128 (32%) coronaries but MPS was found abnormal in 9 (7%) coronaries. Insignificant CAD was noted in 169 (43%) coronaries amongst which reversible ischaemia was noted in 23 (14%). Significant CAD was noted in 99 (25%) coronaries of which only 54 (55%) were MPS positive for reversible ischaemia. The MSCT has a negative predictive value (NPV) of 97%. When MSCT was normal, MPS was almost normal, but the reverse was not true. That is when MPS was normal MSCT was not always normal but showed lesion of insignificant obstruction. In the subset of 33 patients, who underwent invasive angiogram, 132 coronaries were evaluated. Coronary angiogram showed 48 coronaries (36%) to have significant CAD (>50% diameter stenosis). Multislice computed tomography correlated well in 46 (84%) with P value of <0.001 (χ(2)-test) but for 9 (16%) showing overestimation due to increased CACS (>800). Myocardial perfusion single photon emission computed tomography was normal in 15 (27%) coronaries. CONCLUSIONS Myocardial perfusion single photon emission computed tomography provides functional information of the anatomical lesions and MSCT provides anatomical information. Both are two different diagnostic modalities. The MSCT has high NPV in patients with less likelihood for CAD. When compared with CAG, the correlation with MSCT was good and is useful where the calcium score is low.