We present a custom Fourier Domain Optical Coherence Tomography (FDOCT) system adapted to imaging the retinal structures in mice. The FDOCT system utilized spectrometer detection, and operated at a central wavelength of 826nm with a FWHM spectral bandwidth of 72nm, corresponding to an axial resolution of ~4microns (in air). A custom hand-held probe was constructed providing adjustable focusing and increased maneuverability over fixed systems to facilitate coupling of the raster scanned beam into the mouse eye. Image acquisition and display was performed in real time using custom written, multi-threaded software package which displays two dimensional B-scans. Cross sectional images of mouse retina, acquired in vivo an anesthetized animals, are presented.