The High Altitude Balloon Experiment (HABE) is being developed by the U.S. Air Force Research Laboratory, Space Vehicle Directorate at Kirtland Air Force Base, to investigate technologies needed to perform acquisition, tracking, and pointing (ATP) functions against boosting missiles in near-space environments. HABE is designed to demonstrate ATP sequence steps that start with acquisition of a missile plume, transition through passive IR tracking of the plume, and handover to precision tracking, which employs an active laser illuminator and imaging camera to image and track the missile nose. The Inertial Pseudo Star Reference Unit (IPSRU) provides inertially stabilized line-of-sights (LOSs) for the illuminator laser, active fine track (AFT) camera, and the marker scoring. The latter serves to measure and score the payload's pointing performance. The payload will be operated and carried aloft under a large, scientific balloon. The engagement parameters and timelines for the HABE AlP payload are consistent with scenarios encountered in space-based missile defense applications.In HABE experiments, target missiles will pass at ranges from 50 to 200 km. The performance goals of the ATP payload's LOS stabilization and marker laser pointing are required to exceed 1 microradian RMS or better in jitter, drift, and accuracy (two-axis, one sigma metrics), a requirement which stresses testing capabilities. This paper describes an integration and test program that verifies correct performance ofthe HABE ATP payload in its state-of-the-art alignment, stabilization, and tracking functions. In contrast to earlier ATP designs that used analog electronics for control systems implementations, the HABE control systems architecture employs multiple digital processors and coprocessors to measure sensor outputs and generate actuator commands. It is feasible to test all of these digital, multirate control systems by using software procedures that are more autonomous and flexible than the traditional equipment employed for system tests. New, innovative real-time built-in-test algorithms and procedures have been devised to measure performance characteristics of each HABE AlP control system and to confirm its readiness for flight missions. Software connections inject stimulus signals, and the response signals from the digital control system are evaluated in real-time for pass/fail criteria of built-in-test functions. Additionally, test results may be conveyed to ground work stations where the payload performance can be analyzed and compared to design requirements. The paper provides the basis for the test procedures and presents illustrations of its application for tests of the HABE 500 Hz optical autoalignment control system, the inertial LOS stabilization, and the precision active tracking loop.