Virgin olive oils from the fruits of Croatian autochthonous varieties Oblica, Lastovka and Levantinka were characterized for the first time. Headspace volatiles were analyzed by HS-SPME/GC-FID/MS. The main volatiles were C6 compounds. The most abundant was (E)-hex-2-enal (62.60%-69.20%). (Z)-Hex-3-enal was not found in Lastovka oil, while Levantinka oil did not contain hexanal. Tocopherols, chlorophylls and carotenoids were determined by HPLC-FL. Levantinka oil was characterized by the highest α-tocopherol level (222.00 mg/kg). Total phenolic contents (TPs), as well as antioxidant activity (DPPH assay) of the oils hydrophilic fractions (HFs) were assessed by spectroscopic methods. The antioxidant activity of Oblica oil HF was the most pronounced (0.91 mmol TEAC/kg) and the HF contained the highest TPs amount (212.21 mg/kg). HFs phenolic composition was determined by HPLC-DAD. The main identified phenols were secoiridoids dominated in Oblica oil: decarboxymethyl ligstroside aglycone (p-HPEA-EDA up to 158.5 mg/kg), oleuropein aglycone (3,4-HPEA-EA up to 96.4 mg/kg) and decarboxymethyl oleuropein aglycon (3,4-DHPEA-EDA up to 93.5 mg/kg).