This report prepared by the Lawrence Berkeley National Laboratory describes a total cost of ownership model for emerging applications in stationary fuel cell systems. The analysis considers low temperature proton exchange membrane systems for use in combined heat and power applications from 1 to 250 kWe and backup power applications from 1 to 50 kWe. The total cost of ownership framework expands the direct manufacturing cost modeling framework of other studies to include operational costs and life-cycle impact assessment of possible ancillary financial benefits during operation and at end-of-life.