Percutaneous coronary intervention (PCI) of bifurcation lesions remains challenging with a higher risk of adverse outcomes. Whether adjunctive intravascular ultrasound (IVUS) imaging improves outcomes of PCI of bifurcation lesions remains unclear. This study sought to determine the long-term clinical outcomes associated with using IVUS for percutaneous treatment of coronary bifurcation lesions. From April 2003 through August 2010, 449 patients with 471 bifurcation lesions underwent PCI with (n = 247) and without (n = 202) the use of IVUS. Clinical outcomes (death, myocardial infarction [MI], periprocedural MI, stent thrombosis, target vessel revascularization [TVR], and target lesion revascularization [TLR]) were compared between patients undergoing PCI with and without IVUS using univariate and propensity score-adjusted analyses. Most patients (61%) presented with acute coronary syndrome and 89% of bifurcations lesions were Medina class 1,1,1. After propensity score adjustment, use of IVUS was associated with significantly lower rates of death or MI (odds ratio 0.38, 95% confidence interval 0.20 to 0.74, p = 0.005), death (odds ratio 0.40, 95% confidence interval 0.18 to 0.88, p = 0.02), MI (odds ratio 0.37, 95% confidence interval 0.14 to 0.98, p = 0.04), periprocedural MI (odds ratio 0.45, 95% confidence interval 0.20 to 0.97, p = 0.04), TVR (odds ratio 0.28, 95% confidence interval 0.14 to 0.53, p <0.0001), and TLR (odds ratio 0.27, 95% confidence interval 0.14 to 0.53, p = 0.0003) compared to no IVUS. In conclusion, IVUS-guided treatment of complex bifurcation lesions was associated with significantly lower rates of adverse cardiac events at late follow-up. Further study is warranted to evaluate the role of IVUS guidance in improving long-term outcomes after PCI of bifurcation lesions.