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Endometrial receptivity array (ERA)—an objective tool used in assisted reproductive technology—is used for personalized embryo transfer in in vitro fertilization. Hydrosalpinx affects implantation through various mechanisms. However, its effects on ERA are not well established. In this case report, we present the diagnosis and treatment of a 34-year-old nulligravida woman with infertility for two years, obesity, double uterus with unilateral hydrosalpinx and right kidney deficiency. Based on ERA results, endometrial microbiome metagenomic analysis (EMMA), analysis of infectious chronic endometritis (ALICE), and CD138 immunostaining, the patient was treated with hormonal replacement cycle and amoxicillin/clavulanic acid. After one week of amoxicillin/clavulanic acid administration, the vitirified-warmed 4AA blastocyst was transferred to the left uterus—which was absent of hydrosalpinx and easily accessible to transfer and pregnancy was achieved. To the best of our knowledge, this case study is the first one in which we found that there were no differences between the left and right uterus in ERA, EMMA, ALICE, and CD138 immunostainings. Hence, we suggest that hydrosalpinx does not necessarily cause endometrial changes in all cases. Further research to evaluate the effects of hydrosalpinx on implantation with ERA and EMMA/ALICE is warranted.