To compare deep anterior lamellar keratoplasty (DALK) with penetrating keratoplasty (PK) in eyes with corneal diseases not involving the corneal endothelium (keratoconus, scars after infectious keratitis, stromal dystrophies, and trauma). Retrospective, comparative case series. One hundred forty-two consecutive DALK (DALK group; big-bubble technique or manual lamellar dissection using a slitlamp) and 142 matched PK (PK group). Three models were used to describe the postoperative outcomes of the endothelial cell density. A joint regression model was used to predict long-term graft survival. Visual acuity, ultrasound pachymetry, specular microscopy, and optical coherence tomography (OCT) findings were recorded. Postoperative endothelial cell loss and long-term predicted graft survival. The average 5-year postoperative endothelial cell loss was -22.3% in the DALK group and -50.1% in the PK group (P<0.0001). The early- and late-phase annual rates of endothelial cell loss were -8.3% and -3.9% per year, respectively, in the DALK group and -15.2% and -7.8% per year in the PK group (P<0.001; biphasic linear model). The median predicted graft survival was 49.0 years in the DALK group and 17.3 years in the PK group (P<0.0001). The average visual acuity was lower in the manual dissection subgroup compared with the PK group (average difference, 1.0 to 1.8 line) and with the big-bubble subgroup (average difference, 2.2 to 2.5 lines). The average central corneal thickness at 12 months was 536 μm in the PK group, 523 μm in the big-bubble subgroup, and 562 μm in the manual dissection subgroup (P<0.001). The average thickness of the residual recipient stroma measured by OCT was 87±26 μm in the manual dissection subgroup. No correlation was found between this figure and logarithm of the minimal angle of resolution at any postoperative time point (P>0.05). Long-term, model-predicted graft survival and endothelial densities are higher after DALK than after PK. The big-bubble technique gives better results than manual dissection and PK. Compared with PK, manual dissection provides higher survival of both the corneal endothelium and graft, but lower visual acuity.