Aim To observe the effect of melatonin deficiency on macrophage cholesterol efflux and the risk of atherosclerosis in pinealectomized rats. Methods Melatonin deficiency rats （n＝16） were created by pinealectomy （Px）, and compared with sham-operated rats （n＝14）. Blood was drawn at the 0^th week and the 12^th week after surgery to measure serum lipids, glucose and insulin levels. Macrophages were collected at the 0^th and 12^th weeks to measure cholesterol efflux rate and ATP-binding cassette transporter A1 （ABCA1） expression. Results At the 12^th week after surgery, the body weight, serum triglyceride （TG）, very low density lipoprotein cholesterol （VLDLC）, free fatty acide （FFA） and glucose levels were prominently changed in Px rats compared to those in sham-operated rats at the 12^th week （P<0.05）. The ABCA1 mRNA expression was significantly decreased in Px group compared to sham-operated group （P<0.01）. The differences of serum-induced and apolipoprotein A1-induced cholesterol efflux rates between 0^th and 12^th weeks in Px group were both significantly lowered compared to those in sham-operated group （P<0.01）. Conclusions Melatonin deficiency promotes the metabolism abnormality of blood lipids and glucose, and attenuates ABCA1-mediated cholesterol efflux.