With the goal to continue interplanetary exploration and search for past or existent life on Mars, software and hardware for unmanned subsurface drills are being developed. Unlike drilling on Earth, interplanetary exploration drills operate with very low available power and require on-board integrated health monitoring systems, with quick-response recovery procedures, under complete autonomous operations. As many drilling faults are not known a priori, Earth-based direction and control of an unmanned interplanetary drilling operation is not practical. Such missions also require advanced robotic systems that are more susceptible to structural and mechanical failures, which motivates a need for structural health monitoring techniques relevant to interplanetary exploration systems. Structural health monitoring (SHM) is a process of detecting damage or other types of defects in structural and mechanical systems that have the potential to adversely affect the current or future performance of these systems. Strict requirements for interplanetary drilling missions create unique research problems and challenges compared with SHM procedures and techniques developed to date. These challenges include implementing sensors and devices that do not interfere with the drilling operation, producing "real-time" diagnostics of the drilling condition, and developing an automation procedure for complete autonomous operations. Thus, the completed thesis work presents basic research leading to the dynamic analysis of rotating structures with specific application to interplanetary subsurface drill systems, and the formulation of an autonomous, real-time, dynamics-based SHM technique for drilling applications. This includes modeling and validating the structural dynamic system, with and without damage or faults, for a prototype interplanetary subsurface drill, exploring the use of Laser Doppler Velocimeter sensors for use in real-time SHM, developing signal filters to remove inherent harmonic components from the dynamic signal of rotating structures, developing an automation procedure with the associated software, and validating the SHM system through laboratory experiments and field tests. The automated dynamics-based structural health monitoring technique developed in this thesis presents advanced research accomplishments leading to real-time, autonomous SHM, and it has been validated on an operating dynamic system in laboratory and field tests. The formulated SHM and drilling operation also met or exceeded all specified requirements. Other major contributions of this thesis work include the formulation and demonstration of real-time, autonomous SHM in rotating structures using Laser Doppler Velocimeter sensors.