AbstractWe performed a survey on the yield, quality, and chemical characteristics of virgin olive oils from two olive varieties in Croatian Istria: Frantoio and Ascolana tenera, on Cherry leafroll virus‐infected and virus‐noninfected trees and on two harvest dates. Free acidity, peroxide value, specific spectrophotometric absorptions at 232 and 270 nm, fatty acid composition, total phenols, o‐diphenols, oil color, and pigments were determined. Infected olives had lower oil yield and maturity index versus healthy ones. Oils from infected fruits had significant lower value of K232 and K270 and very elevated total phenols content compared to those obtained from healthy olives. Infected Frantoio gave a lower content of o‐diphenols than the healthy ones, which is in contrast to infected Ascolana that had higher values. The aim of this study is to determine the chemical changes in virgin olive oils from healthy and infected trees related to virus influence. According to our knowledge, this is the first survey on the possible influence of viruses on olive fruits, oil yield, and virgin olive oil quality.Practical applications: There are only few papers which analyze the influence of viruses on crops (especially influence on wine quality) and their effects on yield or other agronomic parameters. This work evaluates for the first time the impact of Cherry leafroll virus on the quality of virgin olive oil obtained from Frantoio and A. tenera varieties in terms of basic parameters related to the hydrolitic and oxidative status, content in antioxidant compounds, and in pigments as well as in fatty acid composition.