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Cost functions were developed for earthen basins constructed with various lining materials (compacted clay, synthetic, and geo-clay), and lined steel tanks. These cost functions were incorporated into a cash-based partial budget for manure treatment and storage systems. A partial budget allows one to study the cost of a particular portion of the total capital investment for a given enterprise assuming all other variables are held constant. The cash-based partial budget was applied to determine the annual cost per hog sold on finishing farms ranging from 2,000 to 12,800 head for the following storage and/or treatment alternatives: traditional lagoon, lagoon without sludge storage, storage ponds, storage ponds with a geotextile cover, deep pit below a slotted floor, above ground storage tank, and psychrophilic anaerobic digester. The traditional treatment lagoon was not cost-effective for any swine farm. The treatment and storage systems that met the cost criterion for small farms (2,000 to 4,000 head) were slurry storage ponds, slotted floors over a deep pit, and a geotextile covered storage pond. The annual cost for an ambient temperature psychrophilic anaerobic digester followed by a polishing pond was dependent on the design loading rate. Using loading rates in the range of 25 to 50 lb VS/1,000 ft3-day met the cost criterion on finishing farms ranging from 2,000 to 12,800 head.