Abstract Background Chronic total occlusion (CTO) has a negative impact on the left ventricle function and long-term prognosis of the patients after myocardial infarction. Scientific evidence suggests that some patients with CTO develop collateral arteries which provide an alternative source of blood supply to myocardium and can help to preserve myocardial function. One of the factors influencing the formation of collateral circulation is hypoxia, which induces angiogenesis and arteriogenesis. Physical activity is the most effective stimulus for adaptive changes in cardiovascular hemodynamics. However, the use of hypoxia and endurance exercise training on hemodynamic parameters of the heart and angiogenic factors have not been thoroughly studied yet. The aim of the present study was to examine the effect of endurance training under normobaric hypoxia on cardiac-specific troponin T (cTnT), creatinine kinase-myocardial band (CK-MB), heart-type fatty acid binding protein (H-FABP), vascular endothelial growth factor (VEGF), cytokines and cardiovascular function in patients after myocardial infarction. Methods Patients aged 60.4 ± 4.4 years who had undergone angioplasty with stent implantation participated in the study. Due to high risk of the occurrence of side effects cause by normobaric hypoxia only patients with stable coronary diseases (participants of the second stage of cardiac rehabilitation program) were included. The training program included 3 weeks of endurance training in normobaric hypoxia (HypTr) corresponding to an altitude of 2000 m above the sea level (FiO2 = 15.0%; (HYP-123 Hypoxic Generator, LOWOXYGEN Technology GmbH, Germany). The training regimen comprised 5 sessions/week with 5 min of warm-up, 30 min of interval training (intensity 80% of HRpeak) and 5 min of cooling down. Spiroergometry (CORTEX METAMAX 3B analyzer ) was performed using the cardiopulmonary test Electrocardiography and cardiac biomarkers were evaluated before and after the three weeks of the training programme. Results An increase in average distance covered (622.7 ± 119.0 vs. 687.0 ± 126.7 m, p<0.01) and the test duration (10.4 ± 1.0 vs. 11.0 ± 1.7 m, p<0.05) were observed in response to exercise training in hypoxia. CK-MB (p<0.05) and cTnT (p<0.05) levels were lower post-training compared to the pre-training (p < 0.05). Training in hypoxia had a significant effect on hemoglobin (F=14.7 p<0.001), TNF β (F = 8.2 p<0.01) and VEGF (F = 7.4 p<0.1) levels. Left ventricular (LV) function was altered post-training and the alteration was characterized by favorable changes in end-diastolic and end-systolic dimensions and LV ejection fraction (p<0.05). Conclusions Exercise training in normobaric hypoxia had a significant positive effect on the left ventricular function and concentration of the specific cardiac biomarkers, therefore it may play a crucial role in the cardiovascular adaptive mechanisms in patients after myocardial infarction.