Background Computed tomography-guided transthoracic needle aspiration (TTNA) and biopsy (TTNB) is a well established, safe, and rapid method of reaching a definitive diagnosis for most thoracic lesions. The present study aimed to determine the roles of TTNA and TTNB in the diagnosis of pulmonary diseases and to compare the results using these two techniques. Methods TTNB and TTNA were performed in 105 patients admitted to our clinic due to peripheral pulmonary lesions between May 2005 and November 2007. Needle biopsies were performed using 18-gauge Tru-Cut® biopsy needles and aspirations was performed using 18-20-22-gauge Chiba needles. Results Malignant lesions diagnosed by TTNB were non-small cell lung carcinoma (51 patients, 73%), small cell lung carcinoma (nine patients, 13%), malignant tissue (three patients, 5%), lymphoma (two patients, 3%), thymoma (two patients, 3%), plasmacytoma (one patient, 1%), rhabdomyosarcoma (one patient, 1%), and metastasis (one patient, 1%). The malignant lesions diagnosed by TTNA were non-small cell lung carcinoma in eleven patients (92%) and malignant tissue in one patient (8%). Three (100%) of the benign lesions diagnosed by TTNB were granulomas and two (100%) benign lesions diagnosed by TTNA were infarctions. When the diagnostic value of TTNB and TTNA was compared, TTNB was significantly superior. Malignant lesions were identified in 70 (84%) and benign lesions were identified in three (4%) of the 83 patients in the TTNB group. Ten (12%) patients in the TTNB group could not be diagnosed. Malignant lesions were found in 12 (55%) and benign lesions were found in two (9%) of the 22 patients in the TTNA group. Negative results were obtained in eight (36%) patients. The diagnostic sensitivity, specificity, and accuracy of TTNB was calculated to be 92%, 100%, and 93%, respectively (Table 5). The diagnostic sensitivity, specificity, and accuracy of TTNA was 78%, 100%, and 82%, respectively. TTNB had a sensitivity of 92% (70/76) in malignant cases and 100% (3/3) in benign cases, while the sensitivity of TTNA in malignant and benign cases was 75% (3/4) and 67% (2/3), respectively. Conclusion TTNB is a safe and easy procedure which provides a highly accurate diagnosis of benign and malignant lung lesions without causing a significant increase in complication rates.