Background Coronary artery bypass graft (CABG) surgery with cardiopulmonary bypass (CPB) is associated with systemic inflammatory response and endothelial dysfunction. Our hypothesis is that CPB-induced post-operative endothelial dysfunction may be detected using laser Doppler perfusion monitoring (LDPM) in the skin microcirculation. Methods We used LDPM to investigate the subacute effects of the CPB on systemic microvascular reactivity among patients undergoing CABG surgery with CPB. Thirty patients were submitted to the study of skin microcirculation and blood sample collection at baseline (pre-surgery) and at 7 days post-surgical procedure. The skin microcirculation was evaluated by acetylcholine (ACh) and sodium nitroprusside (SNP) iontophoresis, and thermal hyperemia (TH). Plasma levels of nitrite/nitrate were also analyzed, and cytokine profiles were determined using a multiplex system. Results On-pump CABG surgery induced a significant reduction of the increased microvascular dermal flux observed after cumulative doses of ACh iontophoresis and after TH. On-pump CABG surgery did not induce any significant changes in the microvascular flux after cumulative doses of SNP. Patients still presented high levels of interleukin (IL)-6, IL-8, and C-reactive protein, and low bioavailability of nitric oxide 7 days after the CABG surgery with CPB. Conclusion We observed a significant impairment of systemic microvascular endothelial function and well-preserved endothelium-independent vasodilatation in the skin microcirculation of patients 1 week after CABG surgery with CPB. Our results suggest that LDPM is a useful tool for the assessment of on-pump CABG-induced subacute post-operative endothelial dysfunctions.