The aim of this study was to clarify the mechanism underlying the low implantation rate in patients with thin endometrium. Endometrial thickness during postovulation days 5–7 (mid-luteal phase) during a total of 1,035 natural cycles in 205 patients was analyzed retrospectively. We designated patients with endometrial thicknesses ≤ 6 mm as the thin group (n = 12) and those with endometrial thicknesses ≥ 7 mm as the normal group (n = 193), based on the markedly lower pregnancy rate in the thin group (thin: 8.3% vs. normal: 51.3%). Levels of steroid receptor, transforming growth factor α (TGFα) and oxidative stress were compared between the two groups. Oxidative stress was higher in the stroma of thin endometrium. In addition, expression of progesterone and estrogen receptors was higher, and TGF α expression was significantly lower in thin endometrium. Altered regulation of oxidative stress and levels of steroid receptors and TGF α appear to underlie the low implantation rate seen in patients with thin endometrium.