Objective：To investigate the effect of ATP binding cassette transporter A6 (ABCA6) deletion on the metabolic status of mice fed on a ketogenic diet. Methods：ABCA6 knockout (KO) or wild type (WT) mice were placed on normal diet or ketogenic diet for 2 weeks，respectively. Expression of ABCA6 in the liver of mice fed on normal diet or ketogenic diet was determined by Western blot. Body weights were monitored. The blood samples and livers were harvested. Blood glucose and serum triglycerides (TG)，total cholesterol (TCH)，free fatty acids (FFA)，ALT，AST，and beta hydroxybutyric acid (β-HB) were tested. The contents of TG and TCH in the liver were examined. The hepatic expression levels of genes related to metabolism were detected by realtime-PCR. Results：Feeding of ketogenic diet induced expression of ABCA6 in the liver. No significant difference was observed in body weight，blood glucose and the levels of TG，TCH，FFA，ALT，AST，and β-HB in serum of ABCA6 KO or WT mice fed on normal diet. A 2-week ketogenic diet feeding significantly reduced the levels of blood glucose，serum TCH，and serum FFA in ABCA6 KO mice when compared with WT mice. Meanwhile，more TG and higher mRNA levels of FAS，DGAT2，PCK1，and HMGCS2 were detected in the liver of ABCA6 KO mice fed on ketogenic diet. Conclusion：Deletion of ABCA6 impaired the metabolism of mice fed on ketogenic diet. ABCA6 may be involved in the lipid metabolism of the liver.