Abstract Study question Is there a relationship between the serum progesterone and estradiol levels and certain morphological characteristics of human endometrium during the mid-luteal phase? Summary answer Serum progesterone is associated with the stromal edema and the abundance and size of basal vacuoles in the endometrium of women during the mid-luteal phase. What is known already Progesterone and estrogen are essential hormones that are necessary to prepare the endometrium for pregnancy. Their serum concentrations during the mid-luteal phase are important criteria for prediction of successful embryo implantation. In addition, a variety of endometrial morphological markers, such as the presence of pinopodes, subnuclear and supranuclear vacuoles, glandular secretion, and stromal edema have been applied for determination of the window of implantation and endometrial receptivity. However, the relationship between these endometrial morphological characteristics and serum levels of progesterone and estradiol is still scarcely studied. Study design, size, duration This is an observational study of 98 women, 25 to 46 years of age (mean 37 years), who had a blood sample and an endometrial biopsy during the mid-lutheal phase (LH + 7) in a natural cycle. The study was conducted between August 2020 and November 2020. Participants/materials, setting, methods Serum progesterone and estradiol were measured by electrochemiluminescence immunoassay (ECLIA) on the Cobas e411 analyser (Roche Diagnostics, Germany). The following endometrial morphological characteristics were assessed using light microscopy: (1) basal vacuoles (mean size and percentage of vacuolated glandular cells) (2) apical vacuoles (mean size and percentage of vacuolated glandular cells), (3) pinopodes (percentage of luminal epithelium covered in pinopodes), (4) glandular intraluminal secretion (6-level scoring system), (5) stromal edema (6-level scoring system). Main results and the role of chance The serum progesterone levels ranged between 0.39 and 145.3 ng/ml, with a median of 24.36 ng/ml. The serum estradiol levels varied between 26.91 and 842.89 pg/ml with a median of 124.75 pg/ml. The percentage of cells with basal vaculoles ranged from 0 to 90%, with a median of 38.57%, apical vacuoles (0–50%, 16.83%), pinopodes (0–80%, 23.87%), glandular intraluminal secretion (0–80%, 28.57%), and stromal edema (1–6, 1.42). To examine the association between the serum progesterone and estradiol and the studied endometrial morphological characteristics, the Spearman’s Rho Correlation coefficient for non-paramentric data was used. No correlation was found between serum estradiol levels and the studied morphological variables (p > 0.05). In contrast, the serum progesterone concentration showed a significant negative correlation with the percentage of glandular epithelial cells with basal vacuoles (R= - 0.28; p = 0.03), the mean size of the basal vacuoles (R= - 0.24; p = 0.5) and a significant positive correlation with the stromal edema (R = 0.34; p < 0.01). Limitations, reasons for caution The study was limited in sample size. Wider implications of the findings: The results of this study revealed that serum progesterone is more strongly associated with the occurrence of certain endometrial morphological characteristics during the mid-luteal phase than serum estradiol. These findings are valuable for development of new methods for accurate determination of the window of implantation. Trial registration number Not applicable