Abstract Background Unrecognised myocardial infarction (MI) is a subclinical MI that escapes detection during its acute phase and is associated with an adverse prognosis, similar to clinically recognized MI. Previous studies have suggested the unfavourable outlook for men, and to a lesser extend in women. However, thorough investigation regarding sex differences in prognosis of unrecognised MI for various major adverse outcomes is limited. Purpose This study sought to assess sex differences in the long-term prognosis of unrecognised MI with respect to subsequent clinically recognised MI, heart failure, atrial fibrillation, stroke and all-cause mortality. Methods In a population-based cohort study, encompassing three cohorts with extensive follow-up time, MI status was established at baseline by electrocardiography (ECG) and data from medical records. Participants were followed for the outcomes of interest and censored at the incidence date, loss to follow-up, death, or to 1 January 2015, whichever occurred first. Additionally, participants in the unrecognised MI group were censored once recognised MI occurred. Per outcome of interest, multivariable Cox proportional hazards regression analyses were performed to calculate hazard ratios (HR) and corresponding 95% confidence intervals (CI), using participants without MI at baseline as reference group. All analyses were stratified for sex. Results Of the 12,409 participants at baseline, 519 (4.2%) had experienced unrecognised MI (mean age 70 years, 52% women) and 678 (5.5%) recognised MI (mean age 69 years, 28% women). Mean follow-up time was 10.2 years (± 7.9). Unrecognised MI showed a similar association with subsequent recognised MI in women and men (women; HR 1.57 [95% CI 1.05-2.35], men; HR 1.55 [95% CI 1.10-2.18]). In contrast, associations of unrecognised MI with heart failure (women; HR 1.03 [95% CI 0.77-1.39], men; HR 1.59 [95% CI 1.17-2.15]), atrial fibrillation (women; HR 0.89 [95% CI 0.64-1.25], men; HR 1.83 [95% CI 1.35-2.48]), stroke (women; HR 1.21 [95% CI 0.89-1.64], men; HR 1.87 [95% CI 1.35-2.59]) and all-cause mortality (women; HR 1.09 [95% CI 0.94-1.27], men; HR 1.37 [95% CI 1.16-1.62]) were statistically significant solely in men. Conclusions Unrecognised MI determined by ECG is associated with an increased risk of subsequent recognised MI in both sexes. Additionally, in men, it is associated with an increased risk of heart failure, atrial fibrillation, stroke, and all-cause mortality. Future research should prioritize accurate MI diagnosis via ECG and identify key predictors for adverse outcomes, aiding targeted management efforts.