Purpose: To analyze the graft survival rate and stability of the corneal surface in patients who underwent limbal stem cell transplantation. Three surgical techniques were performed based on the origin of the ocular surface lesion: conjunctival limbal autograft (CLAU), living-related conjunctival limbal autograft (lr-CLAL), and keratolimbal allograft (KLAL) transplantations. Methods: Nonrandomized consecutive comparative case series study. Eighty-four patients (90 eyes; 31 women and 53 men; age range: 11–78 years) were included in the study. Mean follow-up was 31.2 months (range: 6–72 months). Patients were divided into three groups: CLAU, lr-CLAL, and KLAL, comprising 21, 26, and 43 eyes, respectively. Graft survival rate and clinical success of the stem cell transplantation was confirmed by impression cytology. The Kaplan Meier survival curve and generalized Peto tests were used for the analyses. Results: Graft survival rate and the regularity of the corneal surface differed significantly between the allo- and autografts. The 3-year and 6-year graft survival rates were 76.1% and 61.9%, respectively, for the autologous transplantation group, and 59.4% and 46.3%, respectively, for the allogeneic transplantation group. Corneal surface restoration correlated with positive staining for corneal epithelial cells in impression cytology. Conclusions: Significantly better long-term outcomes were achieved with autotransplantation of the limbus compared with allogeneic limbal grafts from living-related and cadaveric donors.