The purpose of this study is to evaluate corneal astigmatism and suture-related complications for transplants sutured with nylon and transplants sutured with Mersilene in primary corneal transplants for Fuchs endothelial dystrophy. A retrospective, observational, and comparative study between transplants sutured with either nylon 10-0 or 11-0 (n = 108) or Mersilene 11-0 (n = 58) was done. One hundred sixty-six eyes of 140 patients who received a primary penetrating keratoplasty for Fuchs endothelial dystrophy between 1995 and 2001 at the Rotterdam Eye Hospital in Netherlands were included. Overall, transplant survival did not differ between groups (log-rank test; P = 0.24). During the first 2 years after transplantation, significantly lower astigmatism was seen in transplants sutured with nylon (P = 0.03). Transplants sutured with Mersilene had a significantly higher risk of surgical intervention to correct astigmatism or wound dehiscence after transplantation (hazard ratio, 2.83; 95% confidence interval, 1.34-6.01). Time to first infiltrate, metaplasia (marked scarring along the sutures), or cheesewiring was significantly less in the Mersilene group (P < 0.01). There was a tendency toward a higher risk of complications associated with loose or broken sutures in the nylon group (hazard ratio, 2.00; 95% confidence interval, 0.57-6.98), which was more pronounced after 2 years. During the first years after corneal transplant surgery, Mersilene sutures are associated with a higher risk of complications and more interventions to correct suture-related problems. However, after 2 years, the grafts seem to be able to retain Mersilene sutures with less risk of suture-related complications as compared with grafts with retained nylon sutures. These favorable long-term effects of Mersilene sutures may outweigh its short-term disadvantage in patients with Fuchs endothelial dystrophy.