Frequency domain optical coherence tomography (FD-OCT) allows interferometer topologies with simplified system construction and handling. Problems of dispersion and polarization matching between the sample and reference arms, as well as beamsplitter spectral non-uniformity, are mitigated when the interferometer is wholly contained in the endoscope tip. A common path set-up, using a reference reflection originating from the inside surface of the glass envelope at the distal end of the endoscope, and an alternative approach with more efficient collection of the reference light using a novel beamsplitter design have been developed. High speed (20,000 A-lines/s) ultrahigh axial resolution (2.4 μm) tomograms of mouse colon have been acquired using a 2 mm outer diameter endoscope in vivo. The FD-OCT system uses a compact mode-locked Ti:Al2O3 laser emitting a broad spectrum (160 nm full- width-half-maximum) centered at 800 nm in combination with a CCD based, spectrally sensitive detector.