INTRODUCTION AND OBJECTIVES: Endometriosis is a gynecological disease with a high frequency in the population, usually causing severe and disabling symptoms, leading women to have a low quality of life and high social and economic costs. Despite being considered a benign disease, studies have supported that women with endometriosis may have an increased risk of developing epithelial ovarian cancers. It is a complex and heterogeneous disease in which extrinsic and intrinsic factors, such as genetics, contribute to their development. Genome-wide association studies (GWA) may be essential to find genetic variants associated with the risk of endometriosis. However, in the current literature, there are some conflicting results between these studies. Thus, the aim of the present study was to conduct a systematic review of GWA studies in endometriosis, to describe the genes associated with the disease and single nucleotide polymorphisms (SNPs), and to discuss possible conflicting results between these studies. MATERIAL AND METHODS: This study is a systematic review of GWA studies in endometriosis published until December 31th, 2019 by PubMed database, considering the following descriptors: endometriosis and (“polymorphism” or “SNP” or “genetic polymorphism" or “variants” or “locus”) and (“GWA” or “Genome-wide” or “Genome wide” or “Genetic association study”). The included studies were analyzed with methodological rigor (STROBE and PRISMA) to enable better quality of case-control and meta-analysis studies, respectively. RESULTS AND CONCLUSION: Of the 88 articles found, only 15 were eligible. All articles had adequate quality assessed by the STROBE and PRISMA checklists (77% and 81%, respectively). In total, 35,022 cases of endometriosis and 181,760 controls were analyzed. The number of participants in each study was quite different (171 to 17,045 for cases and 308 to 150,021 for controls), with a predominance of European ethnicity. Most endometriosis cases (86%) were diagnosed by surgery, while selection of the control group was different among studies. Eleven genes/SNPs were associated with endometriosis risk in more than one article (chromosome 1, 2, 6, 7, 9 and 12; WNT4, GREB1, FN1, IL1A, ETAA1, RND3, ID4, NFE2L3, CDKN2B-AS1 and VEZT). SNPs were localized in intergenic and intronic regions, their risk allele frequencies varied among the studies and their results were conflicting. In conclusion, WNT4 rs7521902, GREB1 rs13394619, FN1 rs1250248, IL1A rs6542095 and VEZT rs10859871 variants are highlighted due to high frequency and pathways and function that each gene influences in the development of endometriosis. However, the replication and validation of these variants in different populations are necessary for a better understanding of the endometriosis etiopathogenesis, in order to optimize the diagnosis and improve the efficiency of clinical treatment of the disease.