Background: To evaluate long-term outcomes after endokeratoplasty in patients with endothelial disorders. Material and methods: Fifty-three eyes of 45 patients with vision loss due to Fuchs' corneal dystrophy, pseudophakic bullous keratopathy, bullous keratopathy secondary to glaucoma, and deep stromal scarring. All patients underwent a personally modified microkeratome-assisted technique of endokeratoplasty between June 2002 and September 2008. All surgeries were performed at the Department of Ophthalmology, Medical University of Vienna by one surgeon (CS). Examinations during follow-up included complete eye examination, best-corrected visual acuity testing, ultrasound pachymetry (Pachymeter SP-2000, Tomey Corporation, Nagoya, Japan) as well as endothelial cell count (Noncon ROBO-CA, Konan-Keeler, Kobe, Japan). Results: Mean age was 70 years (ranging from 43 to 95 years). Mean follow-up period for all patients was 32 months (ranging from 1 to 60 months). Mean visual acuity increased from 0.972 logMAR at baseline to 0.278 after 60 months of follow-up (n = 16, p = 0.007). Mean endothelial cell density decreased from 2,797 cells/mm2 at baseline (donor tissue) to 989 cells/mm2 (n = 15, - 65 %, p < 0.001) after 60 months. Postoperative mean corneal thickness increased from 530 μm (n = 32) at month 3 to 586 μm (n = 15, + 11 %, p = 0.003) after 60 months of follow-up. Five eyes (9 %) experienced graft failure and required reoperation with donor exchange. Conclusions: Although new techniques like DMEK/DSAEK nowadays have replaced the endokeratoplasty procedure, long-term results are comparable to the long-term outcome of modern lamellar endothelial procedures. Endokeratoplasty might remain a possible alternative to penetrating keratoplasty in patients with endothelial disorders and scarring of the posterior stroma by providing faster wound healing and better preservation of corneal surface and thus a better rehabilitation of visual acuity. © 2014 Springer-Verlag Wien.