There are different types of biopsies one can receive: bronchial biopsies, transbronchial biopsies, ultrasound-guided needle biopsies, and transthoracic needle biopsies. Bronchial biopsies, ultrasound-guided needle biopsies, and transthoracic needle biopsies are usually taken because of clinically suspected tumor. Three cylinders are recommended for transthoracic needle biopsy, four to eight pieces are recommended for bronchial biopsies, and three to five punches should be done in ultrasound-guided needle biopsy. Rapid on-site evaluation (ROSE) is recommended if logistically possible. This will enable to control the quality of the FNA-derived material, and in case of insufficient tissues, the procedure can be repeated. Transbronchial biopsies are most often taken for the diagnosis of non-tumor diseases. At least four to six pieces are recommended. Ideally these are taken under radiological control. Video-guided or ultrasound-guided systems are available, which increase the sensitivity of this method. However, if the transbronchial biopsy is not representative or nondiagnostic, we recommend to proceed to videothoracic surgery.

The biopsies should be fixed in 4 % neutral buffered formalin for at least 8 h. After that, they should be processed using automated systems. In case of transthoracic needle biopsies, the cylinders should be placed each in separate cassettes. This will enable to select the most appropriate cylinder for molecular analysis and save additional tissue for further analysis.

The thoracic surgeon, the radiologist, and the pathologist should discuss the selection of the biopsy site. It is important to take the biopsy at a site, where the most important radiologic changes are seen. In interstitial pneumonias, these are nodular densities, granulomas, ground-glass opacities, cystic spaces, etc. The tissue should measure at least 3 × 5 × 3 cm. Biopsies from children including newborn can be smaller. The tissue should be fixed by formalin instillation. Take a small syringe and fill it with formalin. Insert the needle into the lung biopsy and gently inflate it by floating the lung with formalin. The tissue should look like lung tissue in full inspiration. Place the tissue into a container with ample formalin and let it fix for at least 8 h before sectioning it.

After fixation, remove the clamps and section the tissue into 6–8 mm thick slices and describe macroscopically whatever morphologic abnormalities are present. Slicing the tissue may be dictated by the probable diagnoses suspected: slicing in a 90^° angle against the pleura surface is most often appropriate; however, in cases of suspected vascular diseases, it is recommended to section the tissue parallel to the pleura surface, to get cross sections of the vessels (see schematic drawing below). After macroscopic inspection, process the slices each in a separate cassette and number them consecutively.