Cell-free DNA (cfDNA) is an emerging biomarker detectable in various bodily fluids, with promising implications across a wide range of clinical domains. Its minimally invasive nature, short half-life, and ability to reflect tissue-specific genetic and epigenetic alterations position cfDNA as a key tool in women’s health diagnostics. This narrative review aims to explore the biological characteristics, release mechanisms, and clinical utility of cfDNA in gynecological cancers, pregnancy-related disorders, and assisted reproductive technologies (ART), highlighting current applications, benefits, limitations, and future perspectives. A comprehensive literature review was conducted using databases including PubMed, Scopus, Web of Science, and Google Scholar. Relevant peer-reviewed articles from January 2005 to March 2025 were analyzed to summarize advances in cfDNA detection techniques, clinical applications, and emerging technologies in women’s health. In gynecology, cfDNA—especially circulating tumor DNA—has shown promise in early cancer detection, mutation analysis, and disease monitoring. In prenatal medicine, fetal cfDNA (cffDNA) in maternal plasma enables highly accurate, noninvasive screening for chromosomal abnormalities and pregnancy complications such as preeclampsia and intrauterine growth restriction. In reproductive medicine, cfDNA derived from follicular fluid and embryo culture media may serve as a novel biomarker for assessing oocyte and embryo quality. cffDNA offers a noninvasive method for fetal genetic evaluation in pregnancy loss cases, enabling the detection of chromosomal abnormalities to inform clinical management. Technological innovations such as fragmentomics, methylation analysis, and artificial intelligence are enhancing the analytical power and clinical relevance of cfDNA. cfDNA offers a transformative, noninvasive approach for improving diagnosis, prognosis, and personalized care in women’s health. While clinical implementation still faces technical and standardization challenges, emerging tools and multi-omics integration are expected to strengthen the role of cfDNA in precision medicine. Future large-scale studies and validation across diverse populations are essential to support its routine clinical adoption.
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