The Medina classification is the most widespread method to describe bifurcation lesions. However, little is known regarding its prognostic impact. Therefore, the aim of this study is to assess the prognostic significance of the Medina classification following percutaneous coronary intervention (PCI). From a prospective registry of 738 consecutive patients undergoing PCI for bifurcation lesions, 505 were treated with second-generation drug-eluting stents (DES). Of these, 407 (80.6%) presented with “true bifurcation” (TB) lesions (Medina class 1.0.1, 1.1.1, 0.1.1) and 98 (19.4%) in all other categories (“non-true bifurcation” = NTB). We compared rates of death and major adverse cardiac events (MACE: cardiac death, myocardial infarction, or target vessel revascularization) at 12 months and 3 years. Patients with TB had lower rates of previous bypass surgery (7.4% vs. 11.2%, p = 0.043). TB lesions were more likely to be calcified (33.9% vs. 28.6%, p = 0.003) and ulcerated (8.8% vs. 4.1%, p < 0.01). At 12 months, mortality was numerically higher for TB PCI (4.1% vs. 2.1%, p = 0.052) and MACE rates were higher (19.2% vs. 10.2%, p < 0.001). At 3 years, both all-cause death (10.1% vs. 5.1%, p = 0.002) and rates of MACE (37.2% vs. 17.6%, p < 0.001) were higher for TB PCI. After performing regression analysis, TB remained an independent predictor for poor outcomes (OR-2.28 at 12 months, CI 1.45–9.50, p = 0.007, OR-3.75 at 3 years, CI 1.52–6.77, p = 0.001 for MACE). In conclusion, TB lesions, according to the Medina classification, portend worse prognosis for patients undergoing bifurcation PCI. This may guide prognostication and decision-making in treatment.