Purpose: To report postoperative complications of conjunctival limbal autograft in patients with unilateral total limbal stem cell deficiency (LSCD). Methods: In this retrospective observational case series, medical charts of 34 patients with unilateral total LSCD with at least 6 months of follow-up were reviewed. Main outcome measure was postoperative complications. Results: The mean follow-up period was 17.2 +/- 6.3 (range, 6-33) months. The postoperative complications observed included conjunctival encroachment over the graft, small graft, graft dislodging, thick graft, improper position, graft edema, ocular surface exposure, progressive horizontal conjunctivalization, and pyogenic granuloma. Persistent epithelial defect occurred in 5 eyes because of ocular surface exposure (n = 2), conjunctival encroachment (n = 1), and small graft size (n = 2). Epithelial defects healed in 4 of them with sectoral vascularization of the cornea. Optical penetrating keratoplasty was performed on 18 eyes with dense corneal opacification. Persistent epithelial defect occurred in 6 eyes with inadvertent cut limbal graft (n = 2), small limbal graft (n = 2), and ocular surface exposure (n = 2). Conclusions: Conjunctival limbal autograft is an effective procedure for anatomical and visual rehabilitation of eyes with unilateral total LSCD. However, it may be complicated by several adverse events. The most common complications are related to the transplanted grafts (size, thickness, position, and alignment) and chronic ocular surface exposure, which may later lead to epithelial breakdown and corneal conjunctivalization.