This study applied an electronic nose (e-nose) to identify specific odour markers in oil extracted from diseased olive fruits. Virgin olive oil (VOO) is a valuable vegetable oil extracted from fresh and healthy olive fruits. Anthracnose, the most important fungal disease of olives worldwide, results in damage to mature olive fruits. The HERACLES II e-nose (Alpha MOS, Toulouse, France) is based on dual fast gas chromatography technology (two columns of different polarities in parallel coupled to two flame ionization detectors). Therefore, two chromatograms are obtained simultaneously, providing a fingerprint of the product to allow an easy comparison of the overall odour profiles of a batch with the target profile. E-nose analysis made it possible to pre-screen specific odour compounds. Comparing the chromatograms showed important differences in the concentrations of volatile compounds between VOO and the oil extracted from diseased fruits. Twelve peaks were highly specific for oil from the diseased fruits. To allow the e-nose to determine the minimum limit of detection of the unique odour compounds, olive oil from healthy fruit was mixed with oil from diseased fruits at different concentrations. Alpha MOS’s AroChemBase library was used to investigate the nature of the unique odour compounds in the oils based on the retention times of the main peaks. Almost all of these compounds were associated with off-odours of oil from diseased olive fruits. These results have shown that specific odour markers in oil extracted from diseased olive fruits can be identified using the e-nose.