The cells in the organ of Corti are highly organized, with a precise 3D microstructure hypothesized to be important for cochlear function. Here we provide quantitative data on the mouse organ of Corti cytoarchitecture, as determined using a new technique that combines the imaging capabilities of two-photon microscopy with the autofluorescent cell membranes of the genetically modified mTmG mouse. This combination allowed us to perform in situ imaging on freshly excised tissue, thus minimizing any physical distortions to the tissue that extraction from the cochlea and chemical fixation and staining might have caused. 3D image stacks of the organ of Corti were obtained from base to apex in the cochlear duct, from which 3D lengths and relative angles for inner and outer hair cells, Deiters' cells, phalangeal processes, and inner and outer pillars were measured. In addition, intercellular distances, diameters, and stereocilia shapes were obtained. An important feature of this study is the quantitative reporting of the longitudinal tilts of the outer hair cells towards the base of the cochlea, the tilt of phalangeal processes towards the apex, and Deiters' cells that collectively form a Y-shaped building block that is thought to give rise to the lattice-like organization of the organ of Corti. The variations of this Y-shaped element along the cochlear duct and between the rows of outer hair cells are shown with the third row morphologically different from the other rows, and their potential importance for the cochlear amplifier is discussed.