Background: Ectopic pregnancy (EP) is a life-threatening condition, for which novel screening tools enabling early accurate diagnosis would improve clinical outcomes. Kisspeptins, encoded by KISS1, play an essential role in human reproduction, at least partially by regulating placental function and possibly embryo implantation. Kisspeptin levels are massively elevated in normal pregnancy and reportedly altered in various gestational pathologies. Yet, the pathophysiological role of KISS1/kisspeptin in EP has not been investigated previously. Methods: Measurements of plasma kisspeptins and KISS1 expression analyses in human embryonic/placental tissue were conducted in EP and their controls (women undergoing voluntary termination of pregnancy, VTOP) during early gestational window (<12-wks). Putative miRNA regulators of KISS1 were predicted in silico, followed by expression analyses of selected miRNAs and validation of repressive interactions in vitro. Circulating levels of these miRNAs were also assayed in EP vs. VTOP. Results: Circulating kisspeptins gradually increased during the first trimester of normal pregnancy, but were massively reduced in EP. This profile correlated with expression levels of KISS1 in human embryonic/placental tissue, which increased in VTOP but remained suppressed in EP. Bioinformatic predictions and expression analyses identified miR-27b-3p and miR-324-3p as putative repressors of KISS1 in human embryonic/placental tissue at <12-wks gestation, when expression of both miRNAs was low in VTOP controls, but significantly increased in EP. Yet, a significant repressive interaction was documented only for miR-324-3p, occurring at the predicted 3'-UTR of KISS1. Interestingly, circulating levels of miR-324-3p, but not of miR-27b-3p, were dramatically suppressed in EP, despite elevated tissue expression of the pre-miRNA, suggesting defective export in EP. A decision-tree model using kisspeptin and miR-324-3p levels was successful in discriminating EP vs. VTOP, with a receiver-operating characteristic (ROC) AUC of 0.95 ± 0.02 (95% CI). Conclusions: Our results document a massive down-regulation of KISS1/kisspeptins in early stages of EP, likely via a repressive interaction with miR-324-3p. Our data identify circulating kisspeptins and miR-324-3p as novel biomarkers for accurate for screening of EP at early gestational ages.