This study examined the effects of dietary quercetin on the fatty acid (FA) profile of rabbit caecotrophes, dissectible fat, Longissimus thoracis et lumborum (LTL) muscle and hindleg (HL) meat. Sixteen male and sixteen female New Zealand White rabbits were fed a control or quercetin-supplemented (2 g quercetin dihydrate/kg feed) diet from 5 to 12 weeks old, then slaughtered. Caecotrophes were collected from the gut, and the dissectible fat, LTL and deboned HL were sampled. Lipids in the samples were transmethylated, then identified and quantified using GC-FID. Quercetin-supplementation increased C18:0 in the fat, and C20:4n-6 in the LTL - suggesting an interaction with endogenous lipid metabolism - but had no effect on the HL and caecotrophes. Sex affected the caecotrophe FAs, but had little effect on the meat's nutritional value. The FA profiles of the LTL and HL differed, but both aligned to nutritional recommendations. The caecotrophe FA profile was indicative of microbial biohydrogenation, but this had minimal effect on the carcass FA.