Endometriosis is a gynecological disorder characterized by the presence of endometrium-like tissue outside the uterine cavity and, in many cases, by a chronic and recurrent clinical course. This review synthesizes current evidence on the genetic risk loci associated with endometriosis, highlighting key genes implicated in hormonal regulation (WNT4, GREB1, FSHB), inflammation (IL1A), and tissue adhesion. Particular attention is given to genetic correlations and causal links between endometriosis and immunological and metabolic pathways, as well as psycho-emotional disturbances and pain phenotypes. Increasing data demonstrate a frequent co-occurrence of genetic risk factors for endometriosis with autoimmune disorders, neuropsychiatric conditions, and insulin-metabolism abnormalities, emphasizing the systemic nature of the disease. The review also summarizes multi-omics investigations—including microbiome, lipidomic, and epigenetic studies—that illuminate the complex interplay between genetic predisposition and environmental influences. Finally, translational perspectives are discussed, ranging from the development of clinically relevant biomarkers to the implementation of personalized therapeutic strategies informed by a patient’s genetic profile. Collectively, these findings advance the understanding of the molecular basis of endometriosis and outline new avenues for individualized diagnosis and management.