BACKGROUND Ultrasound guided transthoracic needle aspiration biopsy has recently been used to obtain specimens for histological diagnosis of pulmonary and mediastinal tumours. Conventional real time, grey scale puncture guiding devices cannot differentiate vascular structures, and clear visualisation of the needle shaft or tip within a desired target is not always possible. This study describes a new built-in colour Doppler ultrasound puncture guiding device and assesses the relative safety of transthoracic needle aspiration biopsy of thoracic tumours by grey scale or colour Doppler ultrasound guidance. METHODS Thirty patients with radiographic evidence of pulmonary (22 patients) or mediastinal tumours (eight patients) underwent ultrasonographic evaluation and transthoracic needle aspiration biopsy by using the colour Doppler ultrasound puncture guiding device (Aloka UST 5045P-3.5). These tumours were initially examined by grey scale ultrasound, and colour Doppler imaging was then used to evaluate the number of blood vessels surrounding and within the target tumour and the possibility of visualisation of the needle shaft or needle tip during the aspiration biopsy procedure. RESULTS The colour Doppler ultrasound guiding device was far superior to the grey scale device for identification of the number of vessels surrounding or within the target tumour (83% v 20%) and for visualisation of the needle shaft or needle tip (80% v 17%). CONCLUSIONS By using the colour Doppler ultrasound puncture device, vascular structures surrounding or within the target tumour can be verified. Visualisation of the needle shaft or tip is also better. Biopsy routes can be selected to avoid puncturing vessels. This approach should be particularly helpful for guiding biopsies of mediastinal tumours, where puncturing the heart or great vessels is a potential complication.