A custom-built OCT system was used to obtain images of the whole mouse eye. We developed a semi-automated segmentation method to detect the boundaries of the anterior and posterior corneal, lens and retinal surfaces as well as the anterior surface of the iris. The radii of curvature of the surfaces were calculated using a conic section fit of each boundary. Image distortions due to refraction of the OCT beam at the successive boundaries were corrected using a ray-tracing algorithm. Corrected ocular distances, radii of curvature of the cornea and lens surfaces, and anterior chamber angle were obtained on 3 C57BL/6J mice. In vivo imaging of the whole eye, segmentation, conic function fits and correction were successful in all three animals. The posterior lens surface of one mouse could not be fit accurately with a conic section. Biometric parameters of C57BL/6J mice compared well with previous published data obtained from histological sections. The study demonstrates the feasibility of quantitative in vivo biometry of mouse models.