In common with other types of complex models, energy system models have opaque structures, making it difficult to understand both changes between model versions and the extent of changes described in research papers. In this paper, we develop the principle of model archaeology as a formal method to quantitatively examine the balance and evolution of energy system models, through the ex post analysis of both model inputs and outputs using a series of metrics. These metrics help us to understand how models are developed and used and are a powerful tool for effectively targeting future model improvements. The usefulness of model archaeology is demonstrated in a case study examining the UK MARKAL model. We show how model development has been influenced by the interests of the UK government and the research projects funding model development. Despite these influences, there is clear evidence of a strategy to balance model complexity and accuracy when changes are made. We identify some important long-term trends including higher technology capital costs in subsequent model versions. Finally, we discuss how model archaeology can improve the transparency of research model studies.