The clinical significance of non-obstructive coronary artery disease is the subject of debate. Our objective was to evaluate the long-term cardiovascular prognosis associated with non-obstructive coronary artery disease in patients undergoing coronary angiography, and to conduct a stratification by sex, diabetes, and clinical indication. We designed a multi-centre retrospective longitudinal observational study of 3265 patients that were classified into three groups: normal coronary arteries (lesion 70%, 1196 patients). During a mean follow-up of 43 months, we evaluated a combined cardiovascular event: acute myocardial infarction, stroke, hospitalization for heart failure, or cardiovascular death. Multivariable-adjusted Cox proportional hazard models showed a worse prognosis in patients with non-obstructive coronary artery disease, in comparison with patients of normal coronary arteries group, in the total population (hazard ratio 1.72, 95% confidence interval 1.23–2.39; p for trend <0.001), in non-diabetics (hazard ratio 2.12, 95% confidence interval: 1.40–3.22), in women (hazard ratio 1.75, 95% confidence interval 1.10–2.77), and after acute coronary syndrome (hazard ratio 2.07, 95% confidence interval 1.25–3.44). In conclusion, non-obstructive coronary artery disease is associated with an impaired long-term cardiovascular prognosis. This association held for non-diabetics, women, and after acute coronary syndrome.