Porcine epidemic diarrhea virus (PEDV) was first detected in the United States in April 2013, spread rapidly, affected most of the swine producing states and caused significant economic losses. In this study, we developed a PCR-based tool to differentiate between viable and non-viable PEDV to assist in the study of risk factors associated with PEDV transmission. PMA (propidium monoazide) is a dye capable of penetrating cell membranes of non-viable organisms. PMA intercalates into the DNA/RNA of structurally damaged viruses, resulting in a higher cycle threshold (Ct) PCR value indicative of non-infectious  virus. In this study, we show that RT-PCR in combination with PMA can be used to differentiate between infectious and heat inactivated PEDV. However, the ability to differentiate infectious from heat inactivated PEDV depends on the conditions set for sample incubation and pre-treatment, type of sample, quantity of genetic material in the sample. In summary, this report demonstrates the differentiation between infectious and heat inactivated PEDV using PCR based methods in combination with intercalating DNA/RNA dyes in an experiment setting. However, more research is needed to evaluate the feasibility of this technique in field samples.