Dysfunction of cartilaginous endplates (CEP) is an important etiologic aspect of intervertebral disc degeneration (IDD) because the endplate has nutritional and biomechanical functions in maintaining proper disc health. In this study, we investigated the regulatory effects of estrogen on degenerated human CEP cells and the involvement of miR-221 in these effects. Normal and degenerated human CEP tissues were collected from patients with idiopathic scoliosis and IDD, respectively. CEP cells were isolated from these tissues. Polymerase chain reaction (PCR) and western blot analysis were performed to detect the expression of specific genes and proteins, respectively. Apoptosis and cell cycle were analyzed by flow cytometry. The results showed that the levels of aggrecan, collagen II, TGF-β and estrogen receptor α (ERα) were decreased in degenerated CEP tissues, while the levels of MMP-3, adamts-5, IL-1β, TNF-α, IL-6, and miR-221 were increased. Treatment of degenerated CEP cells with 17beta-estradiol (E2) increased the expressions of aggrecan and collagen II, as well as the secretion of TGF-β, but decreased IL-6 secretion. Moreover, E2 inhibited the apoptosis, resumed cell-cycle progression in G0/G1 phase, and improved the cell viability. These data indicate that estrogen has protective effect against degeneration of CEP cells. Furthermore, ERα was confirmed to be a target of miR-221 by the luciferase assay. The synthetic miR-221 mimics or knockdown of ERα attenuated the protective effects of E2, but miR-221 inhibitors promoted the protective effects of E2. These results suggest that miR-221 may impair the protective effect of estrogen in degenerated CEP cells through targeting ERα. This study reveals an important mechanism underlying the degeneration of CEP cells.