In the present study, we have used salmon embryos whose continuous exposure to waterborne PFOA or PFOS at 100μg/L started as freshly fertilized eggs, and lasted for a total of 52 days. PFOS and PFOA were dissolved in methanol (carrier vehicle) whose concentration never exceeded 0.01% of total tank volume. Samples were collected at day 21, 28, 35, 52, 49 and 56 after the start of the exposure. Note that days 49 and 56 represent end of exposure and 1 week after a recovery period, respectively. Tissue bioaccumulations were determined by HPLC/MS/MS, steroid hormones, fatty acids (FAs) and lipids were determined by GC–MS, while mRNA expression levels of genes were determined by qPCR in whole body homogenate. We observed that PFOS and PFOA showed a steady increase in whole body burden during the exposure period, with a slight decrease after the recovery period. Calculated somatic indexes showed that PFOA produced increases in heart-, thymus-, liver- and kidney somatic indexes (HSI, TSI, LSI and KSI). PFOA and PFOS exposure produced significant decreases in whole body dehydroepiandrosterone (DHEA), estrone and testosterone at sampling day 21 and a strong increase of cortisol and cholesterol at the end of recovery period (day 56). PFOA and PFOS effects differed with DHEA and estrone. While PFOS decreased DHEA levels, PFOA produced an increase at day 49, and while PFOS decreased estrone, PFOA produced a slight increase at day 56. We observed changes in FA composition that predominantly involved increases in FA methyl esters (FAMEs), mono- and poly-unsaturated FA (MUFA and PUFA) and a decrease in n-3/n-6 PUFA ratio by both PFOA and PFOS. Particularly, an increase in – pentadecenoic MUFA (15:1), two n-3 PUFAs α-linolenic acid [ALA: 18:3 n3] and eicosapentaenoic acid [EPA: 20:5 n-3] and n-6 PUFA: arachidonic acid [ARA: 20:4 n6], docosapentaenoic acid (DPA) by PFOA and PFOS were observed. These effects were associated with changes in mRNA expression of FA elongase (FAE), Δ5-desaturase (FAD5) and Δ6-desaturase (FAD6) genes. In summary, the changes in hormonal and FA profiles may represent cellular and/or physiological adaptation to continuous PFOS and PFOA exposure by increasing membrane fluidity, and/or overt developmental effects. The present findings provide some potential insights and basis for a better understanding on the possible mechanisms of PFCs toxicity in fish.