Guinea pigs are assumed to practice caecotrophy to a higher degree than rats. Studies from leporids suggest that through the practice of caecotrophy, hindgut fermenting species could build up microbial fatty acids (FA) in body tissues. We hypothesized that microbial FA would be detectable in the body tissue of guinea pigs and rats, and this to a higher degree in guinea pigs. Twenty-four rats and guinea pigs were fed with four different pelleted diets (lucerne-, meat-, meat-bone-, insect-based) in groups of six animals for 8 weeks. Perirenal adipose tissue differed in FA composition between the species in spite of the common diets. FA typically associated with microbial activity (saturated FA (SFA; typically 18:0), monounsaturated FA (MUFA; typically trans-fatty acids TFA), and odd- and branched-chain FA (Iso-FA)), were all detected. Guinea pigs had higher SFA levels than rats except on the lucerne diet. Concentrations of 18:0 were higher for guinea pigs on the meat and bone diet. Iso-FA concentrations in guinea pigs exceeded those of rats on all diets. FA profiles with a microbial fingerprint appear—although in low proportions—in the body tissue of both species, and this seemingly to a higher extent in guinea pigs. With respect to whether consumption of rodent meat rich in microbial FA has particular effects on human health as shown for ruminant products, microbial FA concentrations are probably too low to cause any distinct effects.