Background: Progestogen-only’ contraceptives are presented as injections, implants, oral formulations, hormone-releasing intrauterine methods, and emergency contraceptives. The research designed to assess the effect of different progesterone containing contraceptive methods on safety and endogenous progesterone level.Methods: This prospective cohort study was involved 80 healthy fertile females aged 20-35 years with normal menstrual history and had at least one offspring after spontaneous pregnancy. Subjects were classified into four equal groups according to contraceptive method: group D(Depo-Provera®): used the injectable progesterone of 150 mg every 90 days or 3 months, group I: contains 68 mg of etonogestrel implant formerly known as Implanon, group N: used norgestrel (Ovrette®), (each pill containing 0.075 mg of norgestrel) once daily, and group M: used IUD (Mirena) containing 52 mg of levonorgestrel.Results: Group M had higher endogenous progesterone level compared to those who used other contraceptives containing with normal follicle size. Incidence of amenorrhea was significantly lower in group M (20%) than group D (75%), group I (65%), and group N (70%) with an insignificant difference among the other three groups. Continuation rate was significantly higher in group M than other three groups after 6 months. Efficacy was insignificantly different among the four groups.Conclusion: Mirena had low systemic absorption of exogenous progesterone so, it had less effect on endogenous progesterone with better follicle size and low incidence of side effects (amenorrhea) compared to other contraceptives containing progesterone.