The Measurements Of Pollution In The Troposphere (MOPITT) instrument is one of five instruments flying on NASA's Terra (formerly EOS-AM1) spacecraft that was launched in December 1999. This paper describes the MOPITT instrument mechanical configuration and how it was derived based on system considerations and spacecraft interfaces. These system level considerations include contamination control, EMC/EMI, thermal, optical and structural behavior. The key spacecraft interfaces include mechanical mounting, optical field-of-view (FOV), and thermal transfer. In addition, a detailed discussion is provided for the cryogenic region of the instrument that contains detectors, cold optics, warm optics, and active coolers. Special test fixtures were designed and incorporated in this region of the instrument to permit cooling of the detectors during ambient atmospheric conditions. Some of these test fixtures were designed to fly due to the difficulty in removing them. This utility of operating the instrument's cryogenic detectors within the laboratory environment was extremely beneficial during the instrument optical alignment, EMC testing, and special optical system tests. Final configuring (or closeout) of the instrument's cryogenic region for flight was performed to balance contamination and EMC risks. On-orbit data about the effectiveness of this closeout is provided.