Celiac disease is a multifactorial disorder that involves interactions between genetic and environmental factors. Gluten proteins are responsible for the symptoms of celiac disease, but other environmental factors that influence the intestinal ecosystem, including the milk-feeding type and gastrointestinal infections, may also play a role. Moreover, intestinal dysbiosis, characterized by increased Gram-negative bacteria and reduced bifidobacteria, has been detected in celiac disease patients. This review summarizes current knowledge of the associations between the intestinal microbiota and celiac disease and its possible modes of action in pathogenesis. Deeper understanding of these interactions can help redefine how this disorder is investigated.