The aim of the study reported here was to compare complications of lung biopsy in horses and the quality of the lung specimens after biopsy using the manual Tru-Cut biopsy needle (TC) and an automated biopsy needle (ABN). For experiment 1, lung biopsy was performed in 50 horses with one instrument on one side of the thorax, and then with the other instrument on the other side. Postmortem examination was performed in 20 of the 50 horses. Coughing was detected in 10 of 50 horses and epistaxis was observed in 6 of the 50 horses. Endoscopy revealed bleeding into the airways in 16 of 49 horses and in 5 of 49 horses after biopsy with the TC or the ABN, respectively. Use of the ABN induced a significantly smaller amount of bleeding. Pneumothorax was detected by radiography in 1 of 50 horses. Hematoma diameter determined in 7 of 20 horses at postmortem examination, was significantly larger after biopsy with the TC than with the ABN. The quality of the lung specimen was good. In experiment 2, complications after repeated and multiple lung biopsies in 6 horses were evaluated. Moderate epistaxis was observed on 13 of 104 occasions. Bleeding into the airways was detected at endoscopy on 41 of 104 occasions, and pneumothorax was detected during 4 of 104 occasions. Complications such as hematoma at the biopsy site and bleeding into the airways were greater after biopsy with the TC than after use of the ABN. Lung biopsy specimens obtained with the ABN were fairly safe for the animal.