Sugarcane bagasse is a potential source for commercially-viable products such as animal feed, mulch, or fuel. The applications will be determined by the levels of moisture, ash and beneficial chemicals in the bagasse. Manufacturing value-added products will be impacted by microbes, and may require microbial conversion of the substrate. Microbes present in bagasse have potential for conversion of bagasse to beneficial products because they have the ability to metabolize fibers, and to survive the environmental conditions in bagasse. These microbes also have the potential to interfere with the production of desired products. An analysis of both microbes and chemicals present in bagasse is necessary to determine the most viable potential applications. This study evaluates the microbial and physico-chemical properties in sugarcane bagasse samples from three different varieties in a research setting, and samples of mixed bagasse varieties at three factories. All samples were collected in south Louisiana. Stalks from individual varieties were either shredded or passed through a roller mill. The fresh mixed variety bagasse was collected from the final tandem mill at a factory. The stored mixed variety bagasse was collected from piles at the factories. Samples for microbial analysis were grown on two types of growth media. One medium, MRS, selects for Leuconostoc, Lactobacillus, and other microbes that metabolize sugars and produce degradation products. The second medium, NA, allows growth of a broad range of microbes which are present in the cane growing environment. Microbial counts and types were compared across varieties and processing methods, and were correlated with physicochemical analyses. Fuel value of bagasse was significantly reduced when the bagasse was stored uncovered.