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Biodiesel is an alternative diesel fuel consisting of the alkyl monoesters of fatty acids from vegetable oils or animal fats. Currently, most biodiesel is made from soybean oil, methanol, and an alkaline catalyst. However, there are large amounts of fats and oils that are unsuitable for human consumption that could be converted to biodiesel at lower cost. The problem with processing these waste oils is that they often contain large amounts of free fatty acids that cannot be converted to biodiesel using an alkaline catalyst. These free fatty acids react with the alkaline catalyst to produce soaps that inhibit the separation of the biodiesel, glycerin, and wash water. Previous research has developed a process for pretreating these high free fatty acid feedstocks using acid catalysts which do not form soaps. The objective of this study was to construct a pilot plant to produce biodiesel from a wide variety of feedstocks including those with high free fatty acids. A 50-gallon batch pilot plant has been built which can process high free fatty acid feedstocks using an acid-catalyzed pretreatment followed by an alkaline-catalyzed transesterification. Case studies of pilot plant-scale production of biodiesel from soybean oil, yellow grease with 9% free fatty acids, and brown grease with 40% free fatty acids are presented. The effect of varying the reaction parameters is discussed and the separation and washing processes are described. Estimates of the fuel cost using different feedstocks are also provided.