BACKGROUND: There are two main endometrial preparation techniques in frozen embryo transfers. The natural cycle protocol implies using none or minimal hormone agents, whereas artificial cycles are dependent on using adjuvant hormone therapy. ----- OBJECTIVES: The purpose of this study is to compare clinical pregnancy rates following frozen embryo transfers (FET) in natural and artificial cycles. Also, the goal is to analyse clinical pregnancy rates depending on the age of the participants, stages and number of transferred embryos and types of patient infertility. ----- MATERIALS AND METHODS: This paper includes frozen embryo transfers at University hospital “Sveti Duh” in the five year period. Three hundred sixty-nine transfers and three hundred twenty-three patients who met inclusion criteria were included. The main outcome is presented as a clinical pregnancy rate. The rates are compared depending on the endometrial preparation protocol, the age of the patients, stages and number of transferred embryos and type of patient infertility. ----- RESULTS: The study showed clinical pregnancy rates of 32.1% (79/246) in natural and 31.0% (38/123) in artificial cycles, p=0.812. Increased cumulative clinical pregnancy rate was observed in transfers of blastocyst stage embryos, 36.7% (104/283) compared to cleavage stage embryos 15.1% (13/86), p<0.001. In addition, increased cumulative clinical pregnancy rate was observed in transfers of two embryos, 38.8% (45/116) compared to single embryo transfer 28.5% (72/253), p=0.048. ----- CONCLUSION: There was no significant difference found between natural and artificial cycles in frozen embryo transfers. Due to the possible side effects of artificial cycle protocols, in patients with regular menstrual cycles the advantage is to be given to the natural cycle endometrium preparation. Clinical pregnancy rate is to be higher when transferring blastocyst stage embryos compared to cleavage stage. Also, clinical pregnancy rate will be higher when transferring two embryos, but there is an increased risk of multiple pregnancy.