With recent advances in computer and optics engineering, diagnostic endoscopy of the respiratory tract has now entered the era of microscopic imaging [1, 2]. Currently available microendoscopic devices use the principle of confocal fluorescence microscopy, where the microscope objective is replaced by optical fibres, which conduct both the excitation light to the tissue and the tissue fluorescence back from the fibre tip. Such systems analyse the spatial distribution of specific tissue fluorophores, or alternatively exogenous fluorophores, at the interface with the distal part of the optics. Over the last 5 yrs, fluorescence confocal microendoscopy has been successfully applied to the in vivo explorations of the gastric and colonic mucosae, the biliary tract [3–6] and, more recently, to the microscopic imaging of the proximal and distal respiratory systems [7, 8]. Translating confocal microscopy into the clinic for endomicroscopic explorations is the subject of significant scientific efforts [9, 10], which recently ended in the availability of commercial systems for both animal [11–13] and human in vivo explorations [5, 7, 8, 14]. To take into account the problem of both the small size and relative inaccessibility of the human respiratory system, respiratory endomicroscopic systems use the principle of fibred confocal fluorescence microscopy (FCFM) or catheter-based confocal microscopy.