Virgin olive oils (VOOs) obtained from the fruits of Croatian autochthonous varieties Mašnjača and Krvavica were extensively characterized for the first time. Investigated oils were compared with the oil obtained from Italian variety Leccino, grown and processed under the same conditions. Headspace volatile profile, tocopherols, chlorophylls, carotenoids and total phenolic content, peroxide value, % acidity, K232, K270 as well as antioxidant activity (DPPH) of the oils' hydrophilic fractions (HFs) including their phenolic composition were assessed by means of HS-SPME/GC-MS, HPLC-FL, HPLC-DAD and spectrophotometric methods, respectively. Most of the studied quality parameters varied between the cultivars. The main volatile compounds detected in all tested olive oils were the C6 compounds derived from polyunsaturated fatty acids through the lipoxygenase pathway. Krvavica oil was characterized by hexanal (8.8%-9.4%). Leccino oil contained the highest percentage of (E)-hex-2-enal (73.4%-74.0%), whereas (Z)-hex-3-enal (21.9%-25.0%) and (E)-hex-2-enal (27.6%-28.9%) dominated in Mašnjača oil. Leccino oil contained the highest amount of tocopherols (312.4 mg/kg), chlorophylls (7.3 mg/kg), carotenoids (4.2 mg/kg) and total phenols (246.6 mg/kg). The HF of Leccino oil showed the highest antioxidant capacity (1.3 mmol TEAC/kg), while the HFs of Mašnjača and Krvavica oils exhibited the activity of 0.5 mmol TEAC/kg.