AIM: To compare the corneal endothelial cell density (ECD) of clear grafts after penetrating keratoplasty (PK) and deep anterior lamellar keratoplasty (DALK). METHODS: The study included 44 and 54 patients treated with PK and DALK, respectively, between March 2006 and April 2010. Corneal ECD was examined using specular microscopy at postoperative 1, 3, 6, 12, and 18 months, and the values were compared. RESULTS: Corneal ECD reduction in the PK group was 7.4%, 15.2%, 23.5%, and 28.9% at 3, 6, 12 and 18 months respectively after surgery, compared with 4.2 % in the first month (P<0.01). These figures were 3.0%, 6.7%, 7.2%, and 7.7% at 3, 6, 12 and 18 months respectively, compared with 2.2 % in the first month in the DALK group (P>0.05). CONCLUSION: Compared with DALK,PK significantly reduced ECD of the clear grafts. These results suggest that survival of endothelial cells in grafts is better after DALK than after PK.