The potency of the induction of hepatomegaly, peroxisomal β-oxidation and microsomal 1-acylglycerophoshocholine (1-acyl-GPC) acyltransferase was compared among perfluorinated fatty acids (PFCAs) with 6—9 carbon chain length in the liver of male and female mice. All PFCAs examined induced hepatomegaly and peroxisomal β-oxidation and the potency was in the order of perfluorononanonic acid (PFNA), perfluorooctanoic acid (PFOA), perfluoroheptanoic acid (PFHA) and perfluorohexanoic acid (PFHeA) when compared with the relative doses to induce the two parameters. Microsomal 1-acyl-GPC acyltransferase was induced by PFHA, PFOA and PFNA, as was peroxisomal β-oxidation. No significant sex-related difference was observed in the induction of peroxisomal β-oxidation by any PFCAs examined. PFNA and PFOA accumulated in the liver of both male and female mice in a dose-dependent manner. PFHA accumulated in the liver to a lesser extent; little PFHeA accumulated in the liver. Hepatic concentrations of PFNA, PFOA and PFHA were higher in male mice than those in female mice. One linear regression line was confirmed between the activities of peroxisomal β-oxidation and hepatic concentrations of PFHeA, PFHA, PFOA and PFNA in male mice regardless of their carbon chain lengths, and the activities were saturable at the concentrations over approximately 500 nmol/g liver. Similar linear regression line was obtained between the two parameters in female mice. These results suggest (i) that the longer the perfluoroalkyl chain becomes, the more PFCA accumulates in the liver of both male and female mice, (ii) that the accumulated PFCAs induce hepatomegaly, peroxisomal β-oxidation and microsomal 1-acyl-GPC acyltransferase, and (iii) that the difference observed in the accumulation of PFHA, PFOA and PFNA in the liver between male and female mice is not enough to produce obvious sex-related difference in the induction of peroxisomal β-oxidation.