Background Percutaneous coronary intervention (PCI) with bare-metal stenting (BMS) has been reported to be associated with high rates of target-lesion revascularization (TLR) in heart transplant recipients. We aimed to assess the outcome of successful PCI with BMS or drug-eluting stenting (DES) in such patients. Methods Ninety-four consecutive heart transplant recipients with successful PCI of de novo lesions with BMS ( n = 53) or DES ( n = 60) were prospectively followed-up for 3.7 ± 2.5 years after PCI. An angiographic lesion-based analysis at 12-month follow-up and a long-term, patient-based survival analysis were performed. Results The lesion-based analysis within 12 months after PCI showed a reduction of TLR rates with the use of DES (6.6% vs 26.4%, p < 0.01). DES were associated with better preservation of left ventricular function at this time-point. The patient-based, long-term analysis showed sustained local benefit of DES (hazard ratio 4.5 [1.4 to 14.5] for BMS vs DES), but no effect on mortality, remote-site PCI and total revascularization rates. Anti-hypertensive (hazard ratio 0.2 [0.1 to 0.5]) and aspirin (hazard ratio 0.3 [0.1 to 0.8]) therapy, and left ventricular ejection fraction (0.96 [0.94 to 0.98] per percent) were the only correlates of long-term mortality. Conclusions Compared with BMS, DES are associated with a sustained reduction in rates of TLR and could safely be used in heart transplant recipients with coronary artery disease. Despite excellent local effects, DES use failed to reduce mortality. Anti-hypertensive and anti-platelet therapy, and left ventricular function preservation, may be considered as aims of treatment to improve long-term survival in such patients.