Variations of serum biomarkers and bacterial diversity of the gastrointestinal tract in obese patients with diabetes or hypothyroid are poorly understood. The aim of this study was to provide recent findings in this regard. A total of 119 obese patients [17 with diabetes, 23 with hypothyroid, and 79 patients without either diabetes or hypothyroid (control)] were recruited in this study. Serum biomarkers such as biochemical, hormonal (insulin and glucagon), and cytokine levels [interleukin (IL)-6, IL-1β, tumor necrosis factor-alpha, IL-10, and transforming growth factor beta-1 (TGF-β1)] were measured under fasting conditions. Bacterial abundance of gut microbiota was also quantitated by real-time polymerase chain reaction using 16S rRNA gene-based specific primers. Average value of blood sugar (: 0.0184), hemoglobin A1c, insulin, homeostasis model assessment insulin resistance, TGF-β 1, IL-6, IL-1β, interferon gamma ( < 0.001), and phylum [odds ratio (OR): 1.5, : 0.032] was significantly higher in diabetic versus control group. In contrast, the levels of IL-10 ( < 0.001), (OR: 0.6, : 0.058), and (OR: 0.4, : 0.053) were significantly lower in diabetic versus control group. However, there was no statistically significant difference between the values in hypothyroid versus control group either in crude or adjusted models. While there are some relationships between serum biomarkers or bacterial abundance with diabetes prediction in obese patients, this prognostication is less likely in obese patients with hypothyroid. Further investigation is warranted in the application of identified preclinical biomarkers in the diagnosis of diabetes or hypothyroid in obese patients.