Background Hypopyon is common in eyes with fungal keratitis. The evaluation of the clinical features, culture results and the risk factors for hypopyon and of the possible correlation between hypopyon and the treatment outcome could be helpful for making treatment decisions. Methods The medical records of 1066 inpatients (1069 eyes) with fungal keratitis seen at the Shandong Eye Institute from January 2000 to December 2009 were reviewed retrospectively for demographic features, risk factors, clinical characteristics, laboratory findings and treatment outcomes. The incidence of hypopyon, the fungal culture positivity for hypopyon, risk factors for hypopyon and the effect of hypopyon on the treatment and prognosis were determined. Results We identified 1069 eyes with fungal keratitis. Of the 850 fungal culture-positive eyes, the Fusarium species was the most frequent (73.6%), followed by Alternaria (10.0%) and Aspergillus (9.0%). Upon admission, 562 (52.8%) eyes with hypopyon were identified. The hypopyon of 66 eyes was evaluated via fungal culturing, and 31 eyes (47.0%) were positive. A total of 194 eyes had ocular hypertension, and 172 (88.7%) of these eyes had hypopyon (P<0.001), Risk factors for incident hypopyon included long duration of symptoms (P<0.001), large lesion size (P<0.001) and infection caused by the Fusarium and Aspergillus species (P<0.001), The positivity of fungal culture for hypopyon was associated with duration of symptoms and lesion size. Surgical intervention was more common in cases with hypopyon (P<0.001). Hypopyon was a risk factor for the recurrence of fungal keratitis after corneal transplantation (P=0.002). Conclusions Hypopyon is common in patients with severe fungal keratitis and can cause ocular hypertension. About half of the hypopyon cases were positive based on fungal culture. Long duration of symptoms, large lesion size and infection with the Fusarium and Aspergillus species were risk factors for hypopyon. The presence of hypopyon increases the likelihood of surgical intervention. Chin Med J 2012;125(3):470-475