The ENDOMIX project addresses the urgent need for a comprehensive understanding of the impact of endocrine-disrupting chemicals (EDCs) on human health. Focused on multiple European cohorts, the project employs a unique interdisciplinary approach, leveraging existing robust data and biosamples. By exploring associations and causality between EDC exposure and adverse health outcomes, particularly targeting windows of susceptibility, ENDOMIX seeks to identify health-relevant mixtures of concern. The project integrates high-throughput bioassays and innovative methodologies to examine the immune system’s role in initiating or perpetuating diseases, providing insights into mechanistic pathways and transgenerational impacts. Through the synthesis of in vitro, in silico, and in vivo data, ENDOMIX employs artificial intelligence-assisted knowledge graphs to strengthen causal inference. The project’s findings are poised to contribute essential knowledge to the scientific community, inform policy-making, and raise awareness among citizens about the risks of EDC exposure, ultimately promoting health-preserving behaviors and potentially leading to significant savings in European healthcare systems.