Background Endometrium disorders cause significant failure in fertility. Our study aimed to investigate the cellular, histological, and molecular properties of patients with thin endometrium compared to healthy endometrium without pathological conditions (n = 6). Methods This study was a randomized control (n = 6) in which samples of thin endometrium were obtained from IVF patients enrolled in the IVF clinic in the National Hospital Ciptomangunkusumo, Jakarta, Indonesia, from 2018 to 2019. The typical samples were taken from patients who underwent tubectomy with no pathological findings in the endometrium. Endometrial cells were isolated using an enzymatic method transported in medium, PCR samples were used in an RNA solution, and histology samples were stored in neutral-buffered formalin 10% (v/v). Results The number of cells, presented as density of cells mg−1 wet weight during endometrial biopsy, was about 10,190 cells mg−1 wet weight in the healthy-endometrium group, while the thin-endometrium group had 3305 cells mg−1 wet weight. A flow cytometry analysis of the endometrial in the healthy group showed all panels were significantly higher compared to the thin group: BCRP1/Breast Cancer-Resistant Protein (74.85 ± 15.63% vs. 15.58 ± 7.19%), ICAM-1/Intercellular Adhesion Molecule or CD54 (35.76 ± 6.23% vs. 7.24 ± 1.65%), PECAM/platelet endothelial cell adhesion molecule-1 or CD31 (29.42 ± 2.16% vs. 4.19 ± 2.03%), and cKit/type III receptor tyrosine kinase or CD117 (27.29 ± 1.93% vs. 5.32 ± 2.38%). The exception was SUSD-2/Sushi Domain Containing Protein-2, although these results were insignificant (1.33 …