This paper reviews the fundamentals of the Exergy Cost Theory, an energy cost accounting methodology to evaluate the physical costs of products of energy systems and their associated waste. Besides, a mathematical and computationally approach is presented, which will allow the practitioner to carry out studies on production systems regardless of their structural complexity. The exergy cost theory was proposed in 1986 by Valero et al. in their “General theory of exergy savings”. It has been recognized as a powerful tool in the analysis of energy systems and has been applied to the evaluation of energy saving alternatives, local optimisation, thermoeconomic diagnosis, or industrial symbiosis. The waste cost formation process is presented from a thermodynamic perspective rather than the economist’s approach. It is proposed to consider waste as external irreversibilities occurring in plant processes. A new concept, called irreversibility carrier, is introduced, which will allow the identification of the origin, transfer, partial recovery, and disposal of waste.