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To describe the clinical features of patients affected with vernal keratoconjunctivitis (VKC) with associated limbal stem cell deficiency (LSCD).In a retrospective observational case series, data relating to 49 eyes of 27 patients with VKC and features of LSCD seen from January 2000 to August 2005 at the Cornea Service of LV Prasad Eye Institute were reviewed. Detailed history, visual acuity at presentation, clinical findings, disease activity, duration of complaints, and extent of LSCD and management were noted. The presence of concurrent keratoconus and other ocular or systemic disorders if any were recorded.During this period, 2225 patients with VKC were seen at our institute. Of the 49 eyes, (1.2%) showed features of LSCD. The mean age was 21.37 ± 10.14 years. The male to female ratio was 4 to 1. Twenty-two cases had bilateral disease, and 5 had unilateral affection. The visual acuity at presentation ranged from hand motions to 20/20. The duration of disease ranged from 1 to 25 years, with a mean of 10 ± 6.66 years. Total LSCD was seen in 33 eyes (67.3%), and partial LSCD was seen in 16 (33%). Disease at the time of presentation was active in 15 cases (55.5%) and was quiescent in 12 cases (44.5%). Pannus resection with amniotic membrane graft was done in 5 eyes. Live-related allolimbal transplantation was done in 6 eyes of 3 patients. VKC patients with or without associated LSCD had similar characteristics, but the age of presentation was lower in patients without LSCD (P = 0.0005, unpaired Student t test), and the duration of disease was shorter (P < 0.0001, unpaired Student t test).LSCD seems to be one of the complications of long-standing VKC, contributing to severe visual impairment in young individuals. The chronic nature and prolonged duration of the disease may be responsible for this secondary ocular surface affection, leading to the clinical manifestation of LSCD.