Parenteral nutrition (PN) provides nutritional support intravenously to individuals who have gastrointestinal (GI) failure or contraindication to enteral feeding. Since the initial development of PN, researchers have developed specialized formulas with complete macronutrients, micronutrients, vitamins, minerals, and electrolytes to support patients’ metabolic needs. These formulas prevent malnutrition and optimize patient health, especially under long-term feeding circumstances. Although PN is commonly used and essential in preterm and malnourished patients, complications associated with PN feeding include gastrointestinal defects, infection, and other metabolic abnormalities such as liver injury and brain related disorders. In this chapter, we highlight an overview of PN and its association with abnormalities of microbiome composition as well as with gastrointestinal (GI), immune, hepatic, and neuronal disfunction. Within the gut, PN influences the number and composition of gut-associated lymphoid tissue (GALT) cells, altering adaptive immune responses. PN also modulates intestinal epithelium cell turnover, secretions, and gut barrier function, as well as the composition of the intestinal microbiome leading to changes in gut permeability. Collectively, these changes result in increased susceptibility to infection and injury. Here, we highlight animal models used to examine parenteral nutrition, changes that occur to the major organ systems, and recent advancement in using enteric nervous system (ENS) neuropeptides or microbially derived products during PN, which may improve GI, immune cell, hepatic, and neuronal function.