Objective: In conventional in vivo microscopy, a three dimensional illustration of tissue is lacking. Concerning the microscopic analysis of the pulmonary alveolar network, surgical preparation of the thorax and fixation of the lung is required to place the microscope's objective. These effects may have influence on the mechanical behaviour of alveoli. Relatively new methods exist for in vivo microscopy being less invasive and enabling an observation without fixation of the lung. The aim of this study was to compare a fibered confocal laser scanning microscopy (FCLSM) with optical coherence tomography (OCT) in a mouse and a rabbit model. Moreover, FCLSM was also used endoscopically in the rabbit model. Methods: Smallest possible thoracic windows were excised at the lower margin of the upper right lung lobe and an interpleural catheter inserted before re-coverage with a transparent membrane foil. The OCT-scanner was positioned by a motor driven translation stage. The imaging was gated to endinspiratory plateau. For CLSM, Fluorescein 0.1% was given into the central venous streak line. The confocal probe with a diameter of 650 μm was carefully positioned at the very same lung region. Images were directly recorded real-time and the observed region qualitatively compared with FD-OCT images. Additionally, in the rabbit model, CLSM was used endoscopically under bronchoscopic sight control. In a post-processing analysis, images taken were analyzed and compared by using an "air index" (AI). Results: In the mouse model, the very same region could be re-identified with both techniques. Concerning alveolar shape and size, qualitatively comparable images could be gained. The AI was 40.5% for the OCT and 40.1% for the CLSM images. In the rabbit, even an endoscopic view on alveoli was possible. Likewise AI was 43.2% for CLSM through the thoracic window and 43.6% from endoscopically. For the OCT an AI of 44.6% was analysed in the rabbit model. Conclusions: Both FD-OCT and CLSM provide high-resolution images of alveolar structure giving depth information that is beneficial to conventional microscopy. CLSM also facilitates endoscopic view on alveoli being well comparable to images gained through a thoracic window.