Knowledge about lung movement in health and disease is sparse. Current evaluation methods, such as CT, MRI and external view have significant limitations. To study respiratory movement for image guided tumour diagnostics and respiratory physiology, we needed a method that overcomes these limitations. We fitted balloon catheters with electromagnetic sensors, and placed them in lung lobes of ventilated pigs. The sensors sensed their position at 40 Hz in an electromagnetic tracking field with a precision of ~0.5 mm. The method was evaluated by recording sensor movement in different body positions and at different tidal volumes. No 'gold standard' exists for lung segment tracking, so our results were compared to 'common knowledge'. The sensors were easily placed, showed no clinically relevant position drift and yielded sub-millimetre accuracy. Our measurements fit 'common knowledge', as increased ventilation volume increased respiratory movement, and the right lung moved significantly less in the right than the left lateral position. The novel method for tracking lung segment movements during respiration was easy to implement and yielded high spatial and temporal resolution, and the equipment parts are reusable. It is easy to implement as a research tool for lung physiology, navigated bronchoscopy and radiation therapy.