Background: The aim of our work was to compare the myocardial perfusion imaging by single-photon emission tomography (MPI-SPECT) as a non-invasive, relatively non-expensive test versus the instantaneous wave-free ratio (IFR) for the evaluation of functional significance of the borderline coronary artery lesions in the view of results of fractional flow reserve (FFR) which is considered the gold standard reference test. Results: Our study was conducted in the Cardiology Department. It included 50 patients with borderline coronary artery lesions; they underwent physiological evaluation by stress/rest myocardial perfusion imaging using followed by an invasive physiological assessment by Instantaneous wave-free ratio (IFR) and Fractional flow reserve (FFR). Finally, the results of both SPECT MPI and IFR were compared to FFR as a gold standard reference. There was a strong (kappa = 0.754) significant (P value < 0.001) agreement between the MPI results and FFR results and the overall agreement was 88%. The sensitivity of the MPI was 81.8%, the specificity was 92.9%, the positive predictive value was 90%, the negative predictive value was 86.7%, the positive likelihood ratio was 11.45, and the negative likelihood ratio was 0.20. There was a strong (kappa = 0.918) significant (P value < 0.001) agreement between the IFR results and FFR results and the overall agreement was 96%. The sensitivity of the IFR was 90.9%, the specificity was 100%, the positive predictive value was 100 %, the negative predictive value was 93.3%, and the negative likelihood ratio was 0.09. Conclusions: The instantaneous wave-free ratio (IFR) may be a valid alternative to fractional flow reserve to assess the functional significance of intermediate coronary lesions. The myocardial perfusion imaging may be an alternative, non-invasive, relatively non-expensive test for the evaluation of the physiological significance of intermediate coronary lesions.