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AIMS IQOS is a novel tobacco product claimed to be safer than conventional cigarette smoking due to the heat-not-burn system. This study aimed to evaluate the acute effects of IQOS smoking on myocardial systolic and diastolic functions and compare the acute impact of IQOS with cigarette smoking. METHODS In this prospective study, twenty-seven healthy participants who were using IQOS were included. Transthoracic echocardiography was performed three times for each participant; before smoking any tobacco product (group1), after IQOS smoking (group 2), after cigarette smoking (group3). In addition to conventional echocardiographic measurements, left ventricle (LV) and right ventricle (RV) strain analyses were performed by speckle tracking echocardiography. RESULTS In comparison with non-smoking status, LV global longitudinal strain (GLS) decreased after IQOS and cigarette smoking (-18.9 ± 2.4% in baseline vs. -17.9 ± 2.4% in IQOS vs. -17.9 ± 2.8% in cigarette smoking; p = 0.003, p = 0.001; respectively). LV global circumferential strain (GCS) reduced after IQOS and cigarette smoking (-19.8 ± 4.4% in baseline vs. -18.3 ± 3.9% in IQOS vs. -17.5 ± 3.9% in cigarette smoking; p = 0.005, p < 0.001; respectively). RV GLS was significantly lower in groups smoking IQOS and cigarette (-23.2 ± 4.6% in baseline vs. -21.4 ± 4.1% in IQOS vs. -19.4 ± 4.1% in cigarette smoking; p < 0.001, p = 0.001; respectively). CONCLUSION IQOS (heat-not-burn) tobacco smoking impairs myocardial systolic and diastolic functions in the acute phase like conventional cigarette smoking. The use of IQOS is rising among young adults in recent years, so further studies should be designed to evaluate the chronic effects of IQOS on myocardial function.