The regenerator is a key component of a pulse tube cryocooler, and is also a major contributor to irreversibility and losses in the cryocooler. In this study a method for the assessment of losses in cryocooler regenerators based on entropy generation is proposed. Pore-level CFD simulations are performed for woven mesh regenerator filler by defining periodically repeating unit cells. Simulations are performed for steady-state (uni-directional) as well as periodic flows. It is shown that entropy generation in periodic flow is significantly higher than in steady flow, and is sensitive to operating parameters as well as small geometric irregularities. It is proposed that by optimization of the microstructure of generator fillers the entropy generation and losses can be minimized.