Mechanical and antibiotic bowel preparation have swung in and out of favor among gastrointestinal surgeons. The evidence is reviewed for mechanical and antibiotic bowel preparation, respectively. However, the emerging microbiome science represents an opportunity to view bowel preparation differently. The role of the microbiome on the gastrointestinal tract in both health and disease is briefly reviewed. A better understanding of the complexity of the microbiome may provide the impetus to improve and evolve current bowel preparation practices.