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Background: Gastric bypass (GB) is an effective treatment for those who are morbidly obese with coexisting type 2 diabetes mellitus (T2DM) or non-alcoholic fatty liver disease (NAFLD). Fibroblast growth factors (FGFs) are involved in the regulation of energy metabolism. Methods: We investigated the roles of FGF 19, FGF 21, and total bile acid among those with morbidly obese and T2DM undergoing GB. A total of 35 patients were enrolled. Plasma FGF 19, FGF 21, and total bile acid levels were measured before surgery (M0), 3 months (M3), and 12 months (M12) after surgery, while the hepatic steatosis index (HSI) was calculated before and after surgery. Results: Obese patients with T2DM after GB presented with increased serum FGF 19 levels (p = 0.024) and decreased total bile acid (p = 0.01) and FGF 21 levels (p = 0.005). DM complete remitters had a higher FGF 19 level at M3 (p = 0.004) compared with DM non-complete remitters. Fatty liver improvers tended to have lower FGF 21 (p = 0.05) compared with non-improvers at M12. Conclusion: Changes in FGF 19 and FGF 21 play differential roles in DM remission and NAFLD improvement for patients after GB. Early increases in serum FGF 19 levels may predict complete remission of T2DM, while a decline in serum FGF 21 levels may reflect the improvement of NAFLD after GB.