To compare the role of fresh and dry preserved amniotic membrane transplantation (AMT) in partial limbal stem cell deficiency (LSCD). 30 Patients of partial LSCD involving <180° of cornea of different age group were divided into 2 groups; group A and B. Clinical diagnosis was made on the basis of presence of conjunctival pannus over cornea and loss of limbal palisades of Vogt. After taking impression cytology from the corneal surface, group A patients underwent conjunctival pannus resection followed by fresh AMT while group B patients underwent dry preserved AMT after resection of pannus. Resected specimens were sent for histopathological confirmation of the conjunctival tissue. Serial follow-ups were done at 1, 2, 4, 8, 12 and 24 weeks interval post-operatively. Pre-operative impression cytology revealed goblet cells in 40 and 53.33 % cases of group A and group B respectively. However, histopathological examination confirmed the presence of conjunctival tissue in all cases. All cases in both the groups maintained stable corneal epithelial surface with amelioration of clinical symptoms except for 1 case in group A. At the end of 24 weeks improvement in visual acuity was observed in 40 % cases in both the groups which was not more than 2 Snellen’s line in any case. Complete regression of superficial vascularisation was observed in 60 and 53.33 % cases in group A and B respectively while deep vascularisation persisted in all at the end of study period. Recurrence of conjunctival pannus at the same site was observed in 13.33 % in both the groups. One patient (6.66 %) developed post-operative infectious keratitis in group A while no major complications were observed in group B. Both fresh and dry AMT is equally effective in the treatment of partial LSCD. However, the utility of AMT is limited in corneas with long standing tissue scarring and vascularisation secondary to partial LSCD.