The MPTflex CARS tomograph is a CE-certified patented medical imaging system based on two-photon excited autofluorescence (AF) and an add-on module for Coherent Anti-Stokes Raman Scattering (CARS). The endogenous fluorescent biomolecules NAD(P)H, flavins, porphyrins, elastin, keratin, and melanin as well as non-fluorescent biomolecules like water and lipids can be imaged within seconds and with submicron resolution. The extracellular matrix protein collagen can be detected by its second harmonic generation (SHG). The signals are induced by two femtosecond near infrared laser beams that are guided through an optical arm to a flexible scan/detection head. AF, SHG and CARS signals are recorded by multichannel PMT detectors with single photon sensitivity. Horizontal sections up to 5 x 5 mm² are obtained by galvoscanning and piezo-driven optics. Additional add-on modules for two-photon FLIM and two-photon microendoscopy are available.