Infertility is a condition characterized by the inability to conceive after at least 12 months of unprotected intercourse, affecting approximately 15% of couples worldwide. Despite numerous known causes, in some cases, the causes remain unknown, resulting in idiopathic infertility. The most commonly used treatments include pharmacotherapy in combination with assisted reproductive techniques. Follicular fluid is the natural environment of the oocyte and analyzing the elements within this fluid enables the assessment of oocyte quality and fertilization potential. Copper and zinc, the most abundant trace elements in the body after iron, are present in the composition of follicular fluid and have numerous functions in the body. Their concentration in the follicular fluid positively correlates with fertilization rates. The hypothesis of this study is that ovarian stimulation alters the concentration of copper and zinc in the follicular fluid of women diagnosed with idiopathic infertility compared to the modification of the natural cycle. The study included 52 patients undergoing assisted reproductive treatment in the Sestre milosrdnice University Hospital Center. 27 patients underwent the procedure in a modified natural cycle, while the remaining 25 patients underwent ovarian stimulation. The concentrations of copper and zinc in the follicular fluid samples were determined using atomic absorption spectrometry and the data were analyzed using the statistical program MedCalc. A statistically significant difference in the concentration of copper and zinc was observed between the two groups of participants, leading to the conclusion that ovarian stimulation increases the concentration of copper and zinc in follicular fluid compared to the modified natural cycle. Increased concentrations of copper and zinc are associated with better oocyte quality and higher fertilization rates, as well as greater activity of superoxide dismutase due to increased oxidative stress in patients undergoing cycle stimulation. Since reference intervals for copper and zinc in follicular fluid are not known, further research is needed to determine the optimal levels of these trace elements in follicular fluid and their impact on oocyte quality and fertilization.