The detection and evaluation of microbial contamination is the goal of many programs in the medical, food, pharmaceutical, and environmental monitoring/biothreat detection industries. Similarly, NASA's Planetary Protection program strives to assess, as well as prevent, microbial contamination in spacecraft assembly facilities and on spacecraft themselves. The development of improved methods and technologies designed to facilitate these common goals is therefore important. This review will focus on instrumentation and techniques currently being utilized or evaluated for use by the Planetary Protection program in the clean room environments of spacecraft assembly facilities. Current sampling technologies (novel sampling instrumentation and different collection materials) were compared with NASA standard protocols under field and controlled conditions. A brief literature review was presented to augment the comparisons. Additionally, as the integrity of sample analyses is directly dependent on both the efficiency of sample collection and the quality of sample processing, a novel nucleic acid extraction instrument was also evaluated. The impact of these new technologies will be discussed with respect to sample collection, processing, and analyses from the low biomass environments present in NASA clean rooms, although the findings may be applied in a broader context to other industries and programs as well as to the development of future integrated biosensors.