A relatively new technology in pulmonary medicine, probe-based confocal laser endomicroscopy of distal airways, which is also called alveoscopy, allows for real-time minimally invasive intraacinar imaging. This method has been developed that special miniprobe can be passed into the distal airway via the working channel of the bronchoscope and provide so called "optical biopsy". The method is based on the natural autofluorescence of pulmonary structures, detecting the elastin scaffold of central and peripheral airways, the structure of alveoli, blood vessels and alveolar macrophages. Taking into account the fact that in vivo endomicroscopy of distal airways is a novel diagnostic technique it needs correlating the obtained data at certain disease with the reference methods for the challenges of our current understanding of interpreting endomicroscopic images. We choose high resolution computed tomography and morphology as such reference methods.