This study was designed to investigate the effects of oestrogen on sarcoplasmic reticulum (SR) Ca2+-ATPase activity and gene expression in ovariectomised rats under the condition of chronic intermittent hypoxia (CIH). Thirty-two female Sprague-Dawley rats were randomly divided into four groups: the normal control group (NC), the CIH group (CIH), the CIH-ovariectomised group (CIH+OVX), and the group of CIH-ovariectomised rats receiving estradiol replacement (CIH+OVX+E2). Rats in the latter three groups were exposed to CIH for 5 weeks. The animals were killed before genioglossus (GG) was rapidly excised, and their body and uterus mass were determined. Estradiol level was detected by radioimmunoassay. SR Ca2+-ATPase (SERCA) activity was observed by detecting inorganic phosphorus ion, and the SERCA mRNA level was measured using real-time quantitative polymerase chain reaction (real-time PCR). It was found that, compared with the NC group, the SERCA activity and mRNA level were remarkably reduced (p<.01) in the CIH group. And compared with the CIH group, the SERCA activity and mRNA level were also significantly reduced (p<.01) in the CIH + OVX group. Meanwhile, the SERCA activity and mRNA level significantly increased (p<.01) in the CIH+OVX+E2 group compared with the CIH+OVX group, but lower than those in the NC group (p<.01). The results showed that CIH could reduce the SERCA activity and mRNA expression, and oestrogen-deficiency could exacerbate this effect; whilst estradiol replacement can partially reverse the effect of CIH in ovariectomised rats.