As the field of Structural Health Monitoring (SHM) expands to spacecraft applications, the understanding of environmental effects on various SHM techniques becomes paramount. In January of 2013, an SHM payload produced by New Mexico Tech was sent on a high altitude balloon flight to a full altitude of 102,000 ft. The payload contained various SHM experiments including impedance measurements, passive detection (acoustic emission), active interrogation (guided waves), and wireless strain/temperature sensing. The focus of this paper is the effect of altitude on the active SHM experiments. The active experiment utilized a commercial SHM product for generation and reception of elastic waves that enabled wavespeed measurements, loose bolt detection, and crack detection through the full profile of the flight. Definite deviations were observed in the data through the stages of the flight which included a ground, ascent, float, and descent phases. Several elements of the high altitude environment can have an effect on the measurement such as temperature and pressure. The flight data was compared against a ground altitude baseline and heavy emphasis is placed on comparing changes in the data with the temperature profile of the flight. Conclusions are drawn on the effect of altitude on wavespeed of elastic waves, crack detection, and the sensing of a loose bolt.