Women are frequently reported to have increased morbidity after presentation with acute coronary syndromes and myocardial infarction; however, whether a greater thrombotic tendency contributes to gender differences in clinical outcomes of urgent percutaneous coronary intervention is unknown. Intraprocedural Thrombotic Events (IPTEs) are defined as new or increasing thrombus, abrupt vessel closure, no reflow or slow reflow, or distal embolization at any time during percutaneous coronary intervention. IPTEs were evaluated in this pooled analysis of 6,591 patients with stent implantation and blinded quantitative coronary angiography (QCA) analysis, from the ACUITY and HORIZONS-AMI trials. We compared major adverse cardiac events (MACE) at in-hospital, 30-day, and 1-year follow-up and major bleeding at 30 days according to gender and the presence or absence of IPTE. IPTE was identified in 507 patients (7.7%), with 119 of 1,744 (6.8%) occurring in women and 388 of 4,847 (8.0%) in men (p = 0.12). IPTE, but not gender, was independently associated with MACE at in-hospital and 30-day follow-up. At 1-year follow-up, the adjusted hazard of MACE was higher in women and in patients with IPTE; however, the risk of MACE associated with IPTE was similar among women and men. There was no significant interaction between IPTE and gender for 1-year MACE or 30-day bleeding. IPTE predicted major bleeding only in women. In conclusion, in acute coronary syndromes, women have increased risk of adverse outcome at 1 year. IPTEs are common, occur at similar frequency, and are associated with similar degree of increased MACE in both genders at short- and long-term follow-up. Higher thrombotic propensity does not offer a mechanistic explanation for the worse outcomes noted in women.