Biochemical production of fuels from cellulosic biomass is dependent on understanding the physiology of microbial cellulose utilization; a field in its infancy as compared with soluble substrate utilization. This is largely due to methodological challenges.  Measurements of cell concentration and growth rate are routine for microbial cultures grown on soluble substrates, but this is not the case for cultures grown on cellulose. We know of no controlled comparisons of the rate of cellulose utilization by cellulolytic microorganisms in the literature.   There are highly standardized methods for measuring the specific activity of cellulose-solubilizing enzymes; whereas, there are no standardized methods for cellulose-solubilizing microbes.  These challenges could be overcome by developing rapid and precise techniques for measuring or inferring cell concentration, substrate concentration, and the rate of cellulose solubilization.  The research presented here attempts to address these challenges.  We are investigating on-line measurements, including optical density, off-gas analysis, base consumption as well as elemental analysis (carbon & nitrogen) augmented by automated sampling.  The automated sampling system we developed for fermentations is controlled by a LabVIEW-based operating system and allows for samples of a specified volume to be taken at arbitrarily-chosen time intervals.  Techniques are being established using Clostridium thermocellum ATCC 27405, and eventually will be applied to other cellulolytic microbes and consortia. Present work was performed on crystalline cellulose (Avicel PH-105), but will be extended to pretreated substrates. Combinations of these techniques can demonstrate precise and near-real time monitoring of the carbon flux during cellulosic fermentations.