The present invention is directed to a cleaning system and methods for cleaning tissue embedding molds. The cleaning system includes a cleaning vessel that holds a cleaning solution. The tissue processing molds are supported by a basket receptacle which is placed inside the cleaning vessel. Cleaning solution is supplied to the cleaning vessel through a supply line. Additional fluids are stored in a reservoir and may be mixed with the cleaning solution in the supply line. Cleaning solution drains from the cleaning vessel through a drain line. A controller controls the opening and closing of valves and the activation or deactivation of a heat source to operate a wash cycle, a rinse cycle, and a dry cycle.