A method to measure the orientations of transparent ellipsoidal particles using digital holographic microscopy (DHM) is proposed in this study. This approach includes volumetric recording and numerical reconstruction at different depths. Distinctive light scatterings from an ellipsoid with different angles of orientation are analyzed. A focus function is applied to obtain a reconstructed image that contains a bright line parallel to the major axis of the projected particle, which provides in-plane orientation information. An intensity profile is collected along the major axis of the projected particle in the direction of the optical axis, and this profile is then utilized to measure the out-of-plane orientation of the ellipsoid. After being verified for an ellipsoid with known orientations, the proposed method is applied to ellipsoids suspended in a pipe flow with random orientations. This DHM method can extract the essential information of ellipsoids and therefore has great potential applications in particle dynamics.