Advances in the knowledge regarding celiac disease have enabled the development of diagnostic markers, such as anti-tissue transglutaminase and anti-deaminated gliadin antibodies. The wide availability of these antibodies, genetic studies of HLA-DQ and duodenal biopsies constitute the pillars necessary for a definitive diagnosis. However, difficulties sometimes arise in both the diagnosis and follow-up of celiac patients, which cannot be resolved using these tools. This article reviews the scientific evidence and possible clinical utility of different biomarkers. This review is structured according to biomarkers that have been evaluated pathophysiologically in relation to intestinal damage or immune response and their potential clinical utility in the diagnosis and follow-up of celiac disease patients.