To examine distribution of high-sensitivity cardiac troponin I (hs-cTnI) and myoglobin in patients with suspected coronary microvascular dysfunction (CMD). This study included consecutive patients with chest pain suspected of CMD. Baseline hs-cTnI, myoglobin, and coronary flow reserve (CFR) were assessed. Patients were categorized by hs-cTnI level using the 99th percentile cutoff (28 ng/L). Multivariable regression analyses evaluated associations with impaired CFR and major adverse cardiovascular events (MACE). Among 1,524 patients, 412 (27.0%) had elevated hs-cTnI. Higher hs-cTnI levels were inversely correlated with CFR. Each 10 ng/L increase in hs-cTnI was independently associated with impaired CFR (adjusted odds ratio 1.32). During a follow-up of 24.5 months, elevated hs-cTnI predicted a higher incidence of MACE (adjusted hazard ratio 2.35). Myoglobin alone was not predictive, but concurrent elevation with hs-cTnI further increased MACE risk. Elevated hs-cTnI is independently associated with worse microvascular dysfunction and adverse outcomes in suspected CMD.