In rats and humans, females have higher liver and/or plasma docosahexaenoic acid (DHA) content than males. We hypothesized that the effect of variation in total fat or essential fatty acid intakes on liver and plasma fatty acid composition would differ between sexes. Rats were fed a low-fat soybean oil (LFS), high-fat soybean oil (HFS), or high-fat linseed oil (HFL) diet for 20 d. There were significant sex differences in LFS rats in proportions of (n-3) and (n-6) fatty acids in plasma and liver contingent on lipid class. Significant diet x sex interactions were observed for eicosapentaenoic acid (EPA), DHA, and arachidonic acid (AA) status. HFL females had a higher proportion of EPA in plasma and liver phosphatidylcholine (PC), DHA in liver triacylglycerol (TAG), and AA in plasma PC than HFS and LFS females. These findings show that the effect of varying dietary fat intake on (n-3) and (n-6) long-chain PUFA (LCPUFA) status is modified by sex. Liver phospholipid and TAG fatty acid product:substrate ratios suggested greater Delta6 desaturase (Delta6D) activity in females than in males. The HFL diet induced higher Delta6D mRNA expression compared with the LFS or HFS diets and HFL females had 10% higher expression of Delta6D mRNA than HFL males. Together, these findings show that sex is an important determinant of the effect of variations in fat and fatty acid intake on LCPUFA status, which may have implications for recommendations for fat and fatty acid intake in humans.