Background Gender and complete revascularisation are known to affect mortality. The objective of this study was to analyse a gender difference in mortality with respect to complete revascularisation for multivessel disease after primary percutaneous coronary intervention (PPCI) in ST-elevation myocardial infarction (STEMI) patients. Method In a prospective consecutive cohort of 1472 patients presenting with STEMI for PPCI, between January 2006 and January 2010, 832 patients with multivessel disease were analysed. The primary outcome was long-term mortality. Results Median follow-up was 3.3 +/- 1.2 years. Complete revascularisation was performed less in females than in males (30 vs. 38 %; p = 0.04). At PPCI, women (27 %, n = 221) were +/- 10 years older (p = 0.001), had more hypertension, renal failure and symptoms of heart failure (all p < 0.01). Cumulative long-term mortality with incomplete revascularisation was higher in females (F: 30 vs. M: 15 %, p = 0.01). After adjustment for baseline characteristics, complete revascularisation (0.84; 95 % CI 0.54-1.32) and gender (1.11; 95 % CI 0.73-1.69) lost significance. Also the gender-by-complete revascularisation interaction was not significant at long term. In women, age under 60 years independently predicted higher mortality (HR 10.09; 95 % CI 3.08-33.08; p < 0.001). Conclusion In STEMI patients with multivessel disease at PPCI, women under the age of 60 years had higher mortality, but in women older than 60 years comorbidity impacted the outcome of revascularisation strategy in the long term.