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Abstract Background Mycotic keratitis is an important cause of corneal blindness world over including India. Geographical location and climate are known to influence the profile of fungal diseases. While there are several reports on mycotic keratitis from southern India, comprehensive clinico-microbiological reports from eastern India are few. The reported prevalence of mycotic keratitis are 36.7%,36.3%,25.6%,7.3% in southern, western, north- eastern and northern India respectively. This study reports the epidemiological characteristics, microbiological diagnosis and treatment outcome of mycotic keratitis at a tertiary eye care center in eastern India. Methods A retrospective review of medical and microbiology records was done for all patients with laboratory proven fungal keratitis. Results Between July 2006 and December 2009, 997 patients were clinically diagnosed as microbial keratitis. While no organisms were found in 25.4% (253/997) corneal samples, 23.4% (233/997) were bacterial, 26.4% (264/997) were fungal (45 cases mixed with bacteria), 1.4% (14/997) were Acanthamoeba with or without bacteria and 23.4% (233/997) were microsporidial with or without bacteria. Two hundred fifteen of 264 (81.4%, 215/264) samples grew fungus in culture while 49 corneal scrapings were positive for fungal elements only in direct microscopy. Clinical diagnosis of fungal keratitis was made in 186 of 264 (70.5%) cases. The microscopic detection of fungal elements was achieved by 10% potassium hydroxide with 0.1% calcoflour white stain in 94.8%(238/251) cases. Aspergillus species (27.9%, 60/215) and Fusarium species (23.2%, 50/215) were the major fungal isolates. Concomitant bacterial infection was seen in 45 (17.1%, 45/264) cases of mycotic keratitis. Clinical outcome of healed scar was achieved in 94 (35.6%, 94/264) cases. Fifty two patients (19.7%, 52/264) required therapeutic PK, 9 (3.4%, 9/264) went for evisceration, 18.9% (50/264) received glue application with bandage contact lens (BCL) for impending perforation, 6.1% (16/264) were unchanged and 16.3% (43/264) were lost to follow up. Poor prognosis like PK (40/52, 75.9%, p < 0.001) and BCL (30/50, 60%, p < 0.001) was seen in significantly larger number of patients with late presentation (> 10 days). Conclusions The relative prevalence of mycotic keratitis in eastern India is lower than southern, western and north-eastern India but higher than northern India, however, Aspergillus and Fusarium are the predominant genera associated with fungal keratitis across India. The response to medical treatment is poor in patients with late presentation.