Introduction: Microvascular and endothelial disorders play a significant role in the pathophysiology of coronary slow flow phenomenon (CSFP). However, according to previous studies, the etiology of CSFP is not completely understood. As CD40 and dipeptidyl peptidase-4 (DPP-4) are reported to play an important role in atherosclerosis process as well as microvascular and the endothelial dysfunction, this study evaluated the role of these two biomarkers in the pathophysiology of CSFP. Methods: One-hundred twenty-nine volunteers who were candidates for angiography and fulfilled the inclusion criteria were selected, including 29 patients with coronary artery diseases (CADs) which had less than 50% stenosis (CAD+,<50%) and without CSF, 22 CAD+patients which had 50-90% stenosis (CAD+, 50%-90%) without CSF, 16 CAD+patients with CSF, 22 patients with CSF without stenosis in their arteries, and 40 healthy individuals as controls. The serum levels of CD40 and DPP-4 were measured by an enzyme-linked immunosorbent assay kit. Results: There was no significant correlation between the serum concentration of CD40 and the thrombosis in myocardial infarction (TIMI) frame count (P=0.571). However, the serum concentration of CD40 in CAD+patients with CSF was significantly higher than the values in patients without CSF (P=0.022). Moreover, the concentration of DPP-4 in different coronary vessels did not exhibit any significant relation with TIMI score (P=0.763). Conclusion: In the present study, no significant correlation was found between the serum concentrations of CD40 and DPP-4 and the mean corrected TIMI frame count (CTFC). Accordingly, further studies with larger population sizes are needed to investigate the correlation between CD40 and DPP-4 serum levels and CSFP.