Abstract Study question Is there any molecular deregulation in the gestational endometrium of women with adenomyosis responsible for adenomyosis-related pregnancy disorders? Summary answer Women with adenomyosis show deregulated molecular mechanisms in their gestational phase endometrium involved in miscarriage, preeclampsia, and pregnancy complications, causing adenomyosis-related infertility. What is known already Women with adenomyosis are characterized by having defective decidualization, altered endometrial receptivity, impaired embryo-maternal communication, implantation failure and higher risk of preeclampsia and miscarriage. However, molecular mechanisms underlying these infertility-related conditions remain unknown, mainly due to the inaccessibility of obtaining and maintaining these endometrial tissues. We have previously established adenomyosis endometrial organoids and differentiated them into gestational phase, demonstrating the maintenance of disease-specific traits. For this reason, here we use the already established adenomyosis organoid platform to describe the molecular mechanisms deregulated during gestational phase involved in adenomyosis-associated pregnancy disorders, which could be possible infertility therapeutical targets. Study design, size, duration Endometrial organoids from eutopic endometrium of adenomyosis and non-disease (control) women (n = 15/group) were established and differentiated into gestational phase (ADENO-GESTorg and CONTROL-GESTorg) by supplementation with ovarian and pregnancy hormones. An RNA-sequencing was performed. DESeq2 was used to identify differentially expressed genes (DEGs), FDR < 0.05. GO and KEGG analysis were performed to study DEGs implication at biologically functional level. QIAGEN Ingenuity Pathway Analysis (IPA) was used to further identify upregulated and downregulated pathways. Participants/materials, setting, methods Endometrial biopsies were obtained by hysteroscopy from adenomyosis and control patients (n = 15/group) at IVI Valencia Clinics. Patients between 18≤45 years old and BMI≤28 kg/m2 diagnosed with adenomyosis (adenomyosis group) or without adenomyosis nor other uterine pathologies (control group) were included in the study. Main results and the role of chance We identified 1999 DEGs (153 upregulated and 1846 downregulated) in ADENO- compared to CONTROL-GESTorg. Between upregulated genes, CXCL14 restricts trophoblast invasion and outgrowth, CYP24A1 is increased in spontaneous miscarriage and preeclamptic placentas, and PTAFR induces preterm delivery in mice (log2 Fold Change [log2FC] = 1.6, 2.4, 0.8). Among downregulated genes, deregulated PGR expression has been related to severe preeclampsia and recurrent pregnancy loss, whereas defects on ZWINT, ESCO2 and MCM6 expression are associated with high incidence of aneuploidy, leading to miscarriage, infertility, and newborn disorders (log2FC = −2.21, -2.57, -2.53, -2.48). Functional analysis showed deregulated functions as blastocyst growth, in utero embryonic development, developmental maturation and response to oxidative stress, standing out for their possible involvement in pregnancy disorders. IPA predicted a significant inhibition of D-myo-inositol metabolism (z score [z] = −0.7) affecting oocyte and embryo quality, VEGF signaling (z = −1.5) disturbing trophoblast adaptation to hypoxia, ERK/MAPK signaling (z = −4.0) causing embryonic lethality due to placental alterations; and significant activation of PPARα/RXRα (z = 0.5) that gives rise to recurrent miscarriage and preeclampsia, p53 signaling (z = 1.1) related with preeclampsia-complicated pregnancies, and RHOGDI and PTEN signaling (z = 3.6, 3.4) both promoting preeclampsia. Limitations, reasons for caution Although organoid platforms faithfully recapitulate tissue of origin characteristics as well as disease-specific traits, they are still in vitro models that need to be translated into in vivo studies to further corroborate the results obtained. Wider implications of the findings Molecular mechanisms involved in impaired embryo development, pregnancy loss, preeclampsia and placental defects are deregulated in gestational phase endometrium of women with adenomyosis. These deregulated mechanisms could be therapeutic target to develop pharmacological treatments to ameliorate adenomyosis-related infertility. Trial registration number not applicable