Effective and rapid detection of nitroaromatic explosive compounds, especially trinitrotoluene (TNT), is very important to homeland security as well as to environmental monitoring of contaminants in soil and water, and landmine detection. In this research, we explore a novel nanoscale flagellar motor based TNT detection system (nFMTNT). The nFMTNT is a bio-hybrid MEMS system which combines genetically engineered flagellar motors and MEMS devices. The system consists of three major components: (1) a non-pathogenic, genetically modified Escherichia coli strain KAF95 with a rotating flagellar filament, (2) a microchannel with tethered cells, and (3) a sub-micron bead attached to a rotating flagellar filament. The operational principle of nFMTNT is based on detecting the change in the rotational behavior of the nanoscale flagellar filament in the presence of TNT. The rotational behavior of flagellar filaments of E. coli KAF95 was shown to be extremely sensitive to the presence of nitrate or nitrite. Normally, the flagellar filaments were locked in to rotate in the counterclockwise direction. However, when a nitrate or nitrite was present in the immediate environment, the filaments cease to rotate. Our results indicate that the threshold concentrations required for this response were 10-4 M for nitrate and 10-3 M for nitrite. This is equivalent to around 10 pg of nitrate and 100 pg of nitrite, based on the dimension of the MEMS-based reaction system used for the experiment (400 μm × 100 μm × 40 μm). These detection limits can be even lower when the size of the system is reduced.