Abstract： Background Drug-eluting stent (DES) could obviously reduce in-stent restenosis, which has been proved by international multi-center clinical trials. However, the types of the lesions for stenting were highly selected in these trials. Up to now, there has been no large scale study on the effect of DES in treating complex lesions in real world. Although REALITY trial was just reported during American College of Cardiology Congress 2005, the entry criteria for lesions were limited to one or two de novo lesions. This study was conducted to compare the short- and mid-term clinical outcomes between sirolimus-eluting stent (CYPHER stent) and paclitaxel-eluting stent (TAXUS stent) in patients with complex lesion. Methods This is a retrospective study. From April 2002 to June 2004, a total of 1061 patients were treated with DES in Fu Wai Hospital, of which, 611 patients (642 lesions with 698 CYPHER stents) were in CYPHER group,and 450 patients (534 lesions with 600 TAXUS stents) were in TAXUS group. There was no significant difference in clinical data and lesion types between CYPHER group and TAXUS group. Results Success rates of stent implantation were 99.2% and 98.8% in CYPHER and TAXUS stent groups respectively. The major adverse cardiac events (MACE) during in-hospital and 6-8-month follow-up were 0.7% and 2.3% in CYPHER stent group versus 1.3% and 3.2% in TAXUS stent group. There was no significant difference in MACE rate between these two groups. Restenosis rate was a little higher in TAXUS stent group than that in CYPHER stent group (14.0% vs 7.3%), but there was no significant difference. The incidence of acute occlusion of side branch after implanting DES in main vessel was 6.9% in CYPHER group and 11.9% in TAXUS group(P<0.05).Conclusions CYPHER and TAXUS DES were safe and effective in patients with complex lesion. Clinical outcomes of CYPHER stent were better than TAXUS stent in bifurcation lesions. There was an increasing tendency in restenosis rate and late thrombosis in TAXUS group as compared with that of CYPHER group.