Gut bacteria are involved in regulating several important physiological functions in the host, and intestinal dysbacteriosis plays an important role in several human diseases, including intestinal, metabolic and autoimmune disorders. Although silver nanoparticles (AgNPs) are increasingly being incorporated into medical and consumer products due to their unique physicochemical properties, studies have indicated their potential to affect adversely the gut bacteria. In this review, we focus on the biotoxicological effects of AgNPs entering the gastrointestinal tract and the relationship of these effects with important nanoscale properties. We discuss in detail the mechanisms underlying the bactericidal toxicity effects of AgNPs and explore the relationships between AgNPs, gut bacteria and disease. Finally, we highlight the need to focus on the negative effects of AgNPs usage to facilitate appropriate development of these particles.