Background: Obesity and metabolic syndrome are highly complex disease states and still needs effective treatment and prevention strategies. Growing evidence suggests that dietary milk proteins and prebiotics plays a role in preventing metabolic disorders; however, the underlying mechanisms are unknown. Objective: This dissertation examines how dietary milk proteins and prebiotics (inulin fiber) affect energy balance, host physiology, and gut microbiota to affect metabolic health. The overall objectives of this thesis include: 1) assess the effects of milk protein components on energy balance and stroke onset in stroke-prone rats; 2) determine the role of prebiotics and gut microbiota in regulation of energy balance in obesity-prone and obesity-resistant rats; 3) assess the combined effects of milk protein components and prebiotic on energy balance in obese rats. Methods: Animal studies were conducted using male wistar-kyoto, spontaneously hypertensive stroke-prone, sprague-dawley (SD), obesity-prone (OP) and obesity-resistant(OR) rats. Energy intake, meal patterns, respiratory quotient, and energy expenditure were measured using CLAMS metabolic chambers. Body composition was measured with magnetic resonance imaging. Intraperitoneal glucose and meal tolerance tests were conducted to measure glucose and plasma hormone concentrations. Gut microbiota was assessed using qPCR and 16S rRNA gene sequencing. Gene mRNA abundance was measured using real-time RT-PCR. Results: The primary findings from our study objectives were: 1) supplementation of dietary casein, whey, or its components lactalbumin and lactoferrin, improved energy balance, prevented neurological deficits, morbidity and renal damage and delayed the onset of stroke in stroke-prone rats; 2) gut microbiota play an indispensable role in mediating prebiotic fiber-induced satiety via its effects on cholecystokinin-A and peptide YY Y-2 receptor signaling in high-fat-fed SD, OP, and OR rats; 3) combination of lactoferrin and inulin additively improved energy balance and decreased body weight and adiposity in diet-induced obese rats. Conclusion: Our results provide evidence for the role of milk protein components and prebiotics in improving metabolic dysfunctions in obesity and metabolic syndrome. The findings from our preclinical studies provide a rationale for clinical trials assessing the effects of milk protein components and prebiotics in the prevention and treatment of obesity and its related metabolic abnormalities.