The terms CFO and CAFO relate to the size of the CFO. All farms with at least 300 cattle, 600 swine or sheep, 30,000 poultry, or 500 horses in confinement are CFOs. A Concentrated Animal Feeding Operation (CAFO) is a CFO that meets the threshold animal numbers for a large CAFO in the chart below. Most of the program's requirements apply to CFOs of all sizes. Some requirements apply only to CAFOs.
http://www.in.gov/idem/cfo/2344.htm