The long-term outcomes of patients with myocardial infarction with non-obstructive coronary arteries (MINOCA) are still not well known. This study aimed to compare the characteristics and outcomes between MINOCA and STEMI patients in a 5-year follow-up. Between 2010 and 2015 we identified 3171 coronary angiography procedures performed due to acute coronary syndrome, from which 153 had a working MINOCA diagnosis, and the final diagnosis of MINOCA was ascribed to 112 (5.8%) patients. Additionally, we matched 166 patients with STEMI and obstructive coronary arteries as the reference group. In MINOCA patients (mean age of 63 years), there were more females (60% vs. 26%,p< 0.001), and patients presented most frequently with NSTEMI (83.9%). Patients with MINOCA had more frequent atrial fibrillation (22% vs. 5.4%,p< 0.001) and higher left ventricular ejection fraction (59 ± 10% vs. 54 ± 10%,p< 0.001) compared to STEMI patients. We observed only a trend for a higher rate of MACE in STEMI patients at 5 years (11.6% vs. 18.7%, HR 1.82, 95% CI 0.91–3.63,p= 0.09). In multivariable Cox regression, only beta-blocker use was a protective factor (a trend observed), with HR 0.33, 95% CI 0.10–1.15,p= 0.082 of future MACE. The outcomes of MINOCA and STEMI patients were comparable in the 5-year follow-up.