In this study, the effect of progesterone use on biomarkers due to abortion complaints in aneuploidy screenings was investigated. Two hundred seventy-six singleton pregnant patients with threatened abortion were enrolled in this retrospective study. The treatment group consisted of patients who received oral, vaginal, or intramuscular progesterone (n=137) while the control group received no progesterone (n=139). The results of the double and triple screening tests of the study groups were compared. Nuchal translucency measurements and pregnancy-associated plasma protein-A (PAPP-A), (MoM) values were significantly lower in the group that received treatment with progesterone compared to the control group (p=0.009 and p<0.001, respectively). Beta-human chorionic gonadotropin (βhCG), (MoM) and alpha-fetoprotein (MoM) were found to be statistically significantly higher in the group receiving oral progesterone treatment compared to the group receiving other types of progesterone treatment (p=0.032 and p=0.001, respectively). The PAPP-A was found to be significantly lower in the oral treatment group (p=0.001). It was also significantly lower in the hydroxyprogesterone caproate treatment group (p=0.013). In the vaginal progesterone treatment group, βhCG was significantly lower (p=0.036) than that in oral treatment group. The study showed that there is a relationship between different progesterone administration routes and fetal aneuploidy screening markers.