As a whole, biological research has recently shifted its focus from reductionism to holistic approaches to study complex systems, a strategy often termed "systems biology". Nutritional research has progressed similarly, incorporating phenotype, genotype, genomics, and bioinformatics into an integrative molecular nutrition research model to study the impact of nutritional status on health and disease. Given the importance of livestock and companion animals as large animal models for humans, many of these genomes including that of the dog, cow, cat, and chicken have been sequenced or are being sequenced by the National Institutes of Health (NIH). Ongoing projects to sequence the canine genome and create a SNP map, in addition to the phenotypic and genotypic similarities and unique breed structure of domestic dogs, continue to increase the experimental power of the dog model. While anatomical and physiological similarities have deemed the dog a useful model for gastrointestinal research for decades, economical and ethical concerns have recently decreased their use in this research field. This review aims to reiterate the importance of the dog model in gastrointestinal research, including the study of prebiotics and aging on intestinal health, analyzing gene expression profiles to better understand intestinal diseases such as inflammatory bowel disease, and performing whole genome association studies to identify genetic loci contributing to complex intestinal diseases.