Advances in percutaneous coronary intervention (PCI) have improved the outcomes of patients with coronary artery diseases. The advent of drug-eluting stents (DES) has dramatically reduced the rate of revascularization. The first-generation DES has yielded the main role of PCI to the second-generation DES; however, many patients had been implanted with the first-generation DES, sirolimus-eluting stents (SES) and paclitaxel-eluting stents (PES). Therefore, it is of importance to detect the long-term clinical outcomes in patients who underwent PCI with SES or PES. We analyzed data from our PCI cohort who underwent PCI with first-generation DES at Juntendo University Hospital between August 2004 and June 2010. The index procedure was analyzed when patients underwent multiple PCIs. Patients who were implanted with both SES and PES were excluded from this study. The study ended on December 31, 2011. The primary outcome was a composite of all-cause mortality and acute coronary syndrome (ACS). The secondary outcome was the rate of target lesion revascularization (TLR) and stent thrombosis. We analyzed data from 861 consecutive patients who underwent implantation of SES or PES. The median follow-up period was 1671 days (interquartile range 1081 and 2105). Kaplan–Meier curves for the primary endpoint did not significantly differ between the two groups (p = 0.8). The incidence of stent thrombosis was 1.4 and 1.8 per 1,000 person-years in the SES and PES groups, respectively (p = 0.9). The rate of TLR was significantly lower in the SES, than the PES group (12.6 and 38.3 per 1,000 person-years, p = 0.03). The rate of TLR was lower in the group treated with SES than PES, but the primary outcome comprising all-cause mortality and ACS was comparable between the two groups.