Background Acanthamoeba keratitis (AK) is not a notifiable disease in Israel, so there are no accurate incidence rates for this condition in Israel. The aim of this study was to estimate the incidence of AK in Israel for the years 2008–2012.

Methods We distributed a survey questionnaire to laboratory managers in Israel. The laboratories were affiliated to medical institutes that either provided ophthalmology services or served community ophthalmology clinics. Our questionnaire requested survey respondents to provide information regarding the methods used to diagnose AK, and the number of positive and negative cultures for Acanthamoebae species performed for each of the years from 2008 to 2012.

Results Six laboratories used non-nutrient agar with Escherichia coli as the culture medium, one used calcofluor-white staining with fluorescent microscopy, and two used PCR for diagnosing AK. Twenty-three AK cases were identified, to give an estimated incidence of 1/1 668 552.

Conclusions AK is mostly attributable to the use of contact lenses. As contact lenses are popular in Israel, we expected a higher incidence rate. A lower than expected incidence rate may indicate insufficient awareness of AK in Israel.