OBJECTIVE To investigate the therapeutic outcomes of deep lamellar keratoplasty (DLKP) and penetrating keratoplasty (PKP) for keratoconus. METHODS Retrospective review of 29 eyes of 29 keratoconus patients, who underwent surgery in Eye & ENT Hospital of Fudan University from April in 2003 to April in 2006. Eleven eyes underwent DLKP and the rest had PKP. Pre- and post-operative visual acuity, astigmatism, complications and post-operative graft status were assessed. RESULTS 82% of patients (9 eyes) in DLKP group gained BCVA better than 0.5, while in PKP group the proportion was just 78% (14 eyes). Postoperative astigmatism of two groups had no statistical significant difference with the value (-4.03 +/- 1.87) D and (-3.43 +/- 2.31) D respectively (DS: t = 2.135, P = 0.460, DC: t = -0.643, P = 0.528). The confocal image of epithelial cell, basal epithelium and Bowman's membrane was similar to that of normal cornea. The stromal cell was a little bit smaller and disordered. The endothelium in DLKP-treated eyes had normal cellular size and shape. There was no statistical significance between the density of operated eyes and contralateral unoperated eyes (2311.72 +/- 439.73) cells/mm2 and (2477.81 +/- 535.92) cells/mm2 respectively (t = 1.060, P = 0.780). However, the endothelial cells in PKP-treated eyes were highly pleomorphic with a decreased cellular density of (1642.17 +/- 583.41) cells/mm2, whereas the contralateral unoperated eyes had endothelium density of (2739.05 +/- 401.77) cells/mm2. The difference was statistical significance (Z = 7.32, P = 0.006). Complication rates were similar for DLKP and PKP, although the classification of the complications varied, being less severe in the DLKP group. CONCLUSIONS DLKP seems to be a safe alternative for patients with keratoconus because of its equivalent effect to PKP. DLKP is more technically challenging but allows the risk of endothelial rejection to be avoided and may reduce the risk of late endothelial failure.