AbstractTwelve volatile compounds were quantified by gas chromatography/mass spectrometry in juices from two Spanish mandarin varieties, Fortuna and Clemenules. Fresh Clemenules juice contained a higher amount of total volatile compounds (61.1 ± 1.1 mg L−1) than fresh Fortuna juice (48.8 ± 2.5 mg L−1), with D‐limonene (97.1%), myrcene (1.7%), sabinene (0.5%), α‐pinene (0.3%) and linalool (0.3%) being the predominant compounds. Pasteurisation of the mandarin juices (20 s at 98 °C) caused a significant reduction (∼12%) in vitamin C concentration. On the other hand, vitamin C was stable during storage of the juices for 60 days in aseptic tanks at 2 °C. Volatile compounds, however, were more affected by storage in aseptic refrigerated tanks (2 °C) than by heat treatment. Pasteurisation caused a mean decrease in the total concentration of volatile compounds of about 18%, while, after a storage time of 60 days, 36% of total volatiles present in the juices after pasteurisation were lost from both Fortuna and Clemenules juices. Significant reductions in the concentrations of D‐limonene, myrcene, sabinene, α‐pinene and linalool were found, while those of α‐terpineol and terpinen‐4‐ol increased. Copyright © 2006 Society of Chemical Industry