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Programmed or medicated frozen embryo transfer cycles rely on exogenous progesterone (P) administration to prepare the endometrium for implantation and maintain pregnancy. Presently, the optimal route and dose of P replacement for frozen embryo transfer are not known. In addition, there is a paucity of data and insufficient understanding regarding the metabolism and actions of P in implantation and pregnancy maintenance. In the present review, we discuss how different P assay methodologies affect the determination of P thresholds for implantation and pregnancy maintenance. In addition, we discuss the importance of free P and its regulation in the endometrium and show the complexity of molecular signaling that is required for P-dependent endometrial receptivity. We concluded that future studies should focus on defining accurate circulating and endometrial P concentrations, both for total and free P, and how these concentrations correlate with endometrial receptivity and clinical outcomes.