Reliability and availability of large industries (e.g. refineries and power plants) is one of the most important topics for research. Evaluating shortage cost for such a system is so valour and difficult problem. This paper concerns to develop a novel mathematical model to calculate the shortage cost for spare parts, in a system with redundant equipment. In this model Failure probability and consequence shortage costs for all working states of system is calculated for an operating time period of the system. The application of model is exemplified by a numerical example. The result of this model can be used to develop spare parts inventory policies.