The gut microbiota is implicated in host metabolism and energy regulation. Germ-free (GF) C57BL/6 mice display decreased adiposity, an effect associated with increased intestinal fasting-induced adipose factor (FIAF) and decreased hepatic lipogenesis. However, whether the altered metabolism observed in the absence of gut microbiota extends to other species, commonly used to examine energy metabolism, is unknown. Thus, we used the GF Fischer 344 rat to examine adiposity and associated alterations in intestinal nutrient chemoreceptors, gut peptide levels, and FIAF expression, as well as markers of hepatic and adipose lipogenesis and adipogenesis. We found that GF rats displayed similar body weights and adiposity relative to controls. GF state was associated with up-regulation of intestinal and hepatic FIAF, decreased expression of hepatic FAS, ACC-1, and SREBP, and increased pAMPK and pACC. However, GF rats displayed reduced adipocyte FIAF, increased lipogenic enzymes, and decreased pAMPK, accompanied by an increase in adipocyte size. These findings show that, despite increased intestinal FIAF and reduced hepatic lipogenesis, adiposity is preserved in the Fisher 344 GF rat, unlike the C57Bl/6J GF mouse, with a shift in increased adipocyte lipogenesis. This also demonstrates that adipose, rather than intestinal, FIAF may have a more prominent role in adiposity.