Micro-optic components and subsystems are becoming increasingly important in optical sensors, communications, data storage, and many other diverse applications. In order to adequately predict the performance of the final system, it is important to understand how the optical elements affect the wavefront as it is transmitted through the system. The wavefront can be measured using interferometric means, however, both random and systematic errors contribute to the uncertainty of the measurement. If an artifact is used to calibrate the system it must itself be traceable to some external standard. Self-calibration techniques exploit symmetries of the measurement to separate the systematic errors of the instrument from the errors in the test piece. If the transmitted wavefront of a ball lens is measured in a number of random orientations and the measurements are averaged, the only remaining deviations from a perfect wavefront will be due to spherical aberration contributions from the ball lens and the systematic errors of the interferometer. If the radius, aperture, and focal length of the ball lens are known, the spherical aberration contributions can be calculated and subtracted, leaving only the systematic errors of the interferometer. This paper develops the theory behind the technique and describes the calibration of a micro-interferometer used to measure the transmitted wavefront error of micro-refractive lenses.