BACKGROUND The purpose of this retrospective study was to compare the results and complication rate in CT guided percutaneous trans-thoracic fine needle aspiration biopsies (FNAB) and core biopsies of lung lesions, and to determine the applicability of these needles. PATIENTS AND METHODS In 242 patients (166 males; 76 females) with mean age of 58.9 years (13-84 years) CT guided biopsies of lung lesions were performed on dual slice CT equipment. The average diameter of lung lesion was 2.9 cm (1.2-6.3 cm). For FNAB's 20 - 22 G Chiba needles and for core biopsies 14 G biopsy needles were used. The samples were sent for the histological analysis. The cytological or histological results and the eventual complications were compared. RESULTS FNAB's cytological samples were adequate for definitive diagnosis in 117 patients (79.60 %) and inadequate in 30 patients (20.40 %). Core biopsies samples were adequate in 92 (96.85 %) patients and non- representative (necrotic tissue) in 3 (3.15 %). Pneumothorax as the most frequent complication was detected in 14 (9.7 %) of the patients in the group of FNAB's and in 30 (31.5 %) of the patients with the core biopsy group. CONCLUSIONS The results showed that percutaneous transthoracic CT guided biopsies of lung lesions were an effective and safe procedure in the diagnosis of lung lesions. Core biopsy gives a higher percentage of representative samples than FNAB, and is a preferred method regardless of the higher rate of complications.