Total body nitrogen (TBN) can be used to estimate total body protein, an important body composition component at the molecular level. A system using the associated particle technique in conjunction with prompt gamma neutron activation analysis has been developed for the measurement of TBN in vivo. The system uses a compact D, T neutron generator (~107 n/s) coupled to an internal alpha-particle detector, and a counting system with six bismuth germinate detectors. 14 Subjects were scanned from shoulders to hips (20 min scan time, <0.4 mSv dose) generating complex spectra dominated by signals from C, O, H, and N, with significant peak overlap. Fractional contributions from these elements to regions of interests (ROI) spanning a 4–8 MeV range were determined by algorithms comparing ratios of interrelated ROIs. In addition, multi-component least squares fitting was done to further resolve individual peak activities (MATLAB R2011b). Total body potassium (TBK) was also measured using a whole body gamma counter. Predicted TBN values, based on fat-free mass estimated from TBK, were compared to measured TBN results. Measured versus predicted results for all subjects were not statistically different. Separating subjects by gender also showed no difference between measured and predicted values. The associated particle system showed good agreement with predicted TBN values, but measurement precision was not better than that commonly seen in traditional prompt gamma thermal neutron activation analysis systems.