OBJECTIVES: Endometrial cancer (EC) is the most common malignancy of the female genital tract in developed countries, yet preventive screening remains unavailable, and diagnostic approaches are largely limited to symptomatic women. Despite advancements in precision oncology, the biology of precancerous lesions is less understood compared to advanced disease. To address this gap, we conducted a prospective case-control study analysing uterine lavage fluid from women undergoing diagnostic evaluation. The study included 257 participants: 80 diagnosed with endometrial intraepithelial neoplasia (EIN), 89 with early-stage EC, and 88 healthy controls. Using targeted next-generation sequencing, we examined genetic alterations in 22 selected genes associated with EC development. RESULTS: Our findings did not confirm a direct association between specific genetic mutations in uterine lavage fluid and the presence of EIN or early-stage EC (p = 0.501). Mutations were detected in both cases and controls, with a higher overall mutation burden observed in controls, suggesting potential background genomic alterations unrelated to EC development. In conclusion, while molecular profiling of uterine lavage fluid remains a promising concept for non-invasive diagnosis, our results highlight significant challenges in specificity. Further studies with larger cohorts and additional biomarkers are necessary to clarify its diagnostic relevance and clinical applicability.