Purpose: To compare the status of corneal endothelium and central corneal thickness within the first four postoperative years after deep anterior lamellar keratoplasty (DALK) and penetrating keratoplasty (PK) in patients with keratoconus. Materials and Methods: Thirty-nine eyes (Group A) which had PK and 44 eyes (Group B) which had DALK for the treatment of keratoconus were included in this retrospective study. The endothelial cell density (ECD), the mean endothelial cell area and the coefficient of variation of cell area were assessed with a non-contact specular microscope, and the central corneal thickness (CCT) was measured with an ultrasound pachymeter. Results: Mean ECD loss rate at two years was 36.24% in Group A and 18.12% in Group B (P<0.001). Mean ECD loss rate at four years was 47.82% in Group A and 21.62% in Group B (P<0.001). Mean annual ECD loss rate was calculated 14.12% per year in Group A and 5.78% per year in Group B. In the PK group, increase in mean CCT was 15.60% in two years and 15.03% in four years, while in the DALK group, mean CCT increased by 8.05% in two years and 9.31% in four years. Conclusions: As the majority of ectatic disorders such as keratoconus occur in young people, long-term endothelial cell survival following treatment with keratoplasty is essential for the long-term visual ability. Our finding that corneal endothelial cell loss in the DALK group occurs at a slower rate than in the PK group suggests DALK as a safer alternative to PK in these selected patients.