The volatile profile of four different groups of dried pistachios namely: H: healthy, NC: naturally contaminated with aflatoxin, AC: artificially contaminated with aflatoxigenic strains of the fungi Aspergillus flavus and ANT: artificially contaminated with non-toxigenic strains of the fungi A. flavus, was determined. The volatiles were isolated by the HS-SPME method and determined by GC–FID and GC–MS, whereas aflatoxin by HPLC. Seventy two volatile compounds were identified almost equally distributed among the above four studied groups. The predominant chemical compounds were monoterpenes, alcohols, ketones, aldehydes, esters and hydrocarbons. The monoterpenes, mainly determined as α-pinene and α-terpinolene were detected in all samples. Even though the general volatile profile was similar among groups, some differences were detected between healthy and contaminated groups of samples. When some key volatiles such as eight-carbon and seven-carbon alcohols and aldehydes were used along with the species-specific sesquiterpenes and the other terpenes detected, a correct classification was obtained in H, NC, AC and ANT groups, as was demonstrated by cluster and discriminant analyses. This evidence provides a potential tool for distinguishing contaminated samples on the basis of characteristic volatile patterns. •Seventy two volatiles were isolated from the volatile profiles of pistachios.•Most volatiles were alcohols, ketones, aldehydes, esters and hydrocarbons.•Monoterpenes were detected in all samples.•The volatiles related to contaminated groups were identified.•Correct classification through multivariate analysis was possible using key volatiles.