In order to explore the effects of progestin levonorgestrel (LNG) on lipid metabolism in fish, newly hatched Chinese rare minnow larvae were exposed to 0.8 and 6.5ng/L LNG for 6months until adults, and the growth parameters, hepatic histopathologic changes, lipids and lipoproteins contents and expression levels of lipid metabolism related genes were investigated. The results showed that the body weights and condition factors of rare minnow at 70dph were significantly decreased by exposure to 0.8 and 6.5ng/L LNG, and the body lengths or body weights were also significantly decreased in females and males at 180dph after exposure to 6.5ng/L LNG. Hepatic damages such as cellular vacuolation and swelling of hepatocytes were induced in adults at 180dph after exposure to 0.8 and 6.5ng/L LNG. The hepatic triglyceride and cholesterol contents in females at 180dph were significantly decreased by exposure to 0.8 and 6.5ng/L LNG, and the serum triglyceride contents were also significantly decreased after exposure to 6.5ng/L LNG, but no effects were observed on male hepatic and serum lipid contents. Besides, the hepatic mRNA expression level of fatty acid synthase gene (fasn) was significantly decreased in females at 180dph by exposure to 0.8 and 6.5ng/L LNG, and the hepatic mRNA expression levels of fasn and acetyl-CoA carboxylase gene (acaca) were also significantly decreased in males at 180dph after exposure to 6.5ng/L LNG. As can be concluded from the results, long-term exposure of rare minnow to low concentrations of LNG inhibited growth, induced hepatic damages, caused sex-specific changes on hepatic and serum lipid contents, and affected mRNA expression of lipid metabolism related genes in the liver. The present study demonstrates that LNG could disrupt lipid metabolism in rare minnow at low concentrations, indicating high potential ecological risks of LNG to fish populations.