Recently, the endomysial antigen has been identified as the protein cross-linking enzyme known as tissue transglutaminase (tTG). Our objective was to compare a novel enzyme immunoassay (EIA) that detects IgA antibody against tTG to two standard IFA methods utilizing thin tissue sections of rat kidney/rat stomach (KS) and distal primate esophagus (PE) as substrates to detect IgA antibody against endomysium (EMA). Sera from 100 patients suspected of having gluten-sensitive enteropathy (GSE) and 23 sera possessing various antibodies used for EIA cross-reactivity studies were included. Additional tests, performed routinely in our laboratory, were utilized to further assess sera from patients suspected having GSE. These tests include anti-gliadin IgA antibody (AGA) and anti-reticulin IgA antibody (ARA) and are part of the European Society for Pediatric Gastroenterology and Nutrition (ESPGAN) revised criteria for diagnosing GSE. When compared to IFA using KS, the tTG EIA had a sensitivity of 87.5%, was 97.1% specific, and had an overall agreement of 94.0%. When compared to IFA using PE, the tTG EIA had a sensitivity of 92.6%, was 93.2% specific, and had an overall agreement of 93.0%. When the KS IFA was compared to the PE IFA for EMA, the KS IFA had a sensitivity of 96.3%, was 91.8% specific, and had an overall agreement of 93.0%. The majority of sera that were positive for tTG but were negative by IFA (KS, n = 2/PE, n = 5) possessed IgA antibodies against gliadin and/or reticulin. Five of six sera with negative results by PE IFA were positive by the KS IFA and possessed one or more antibodies to tTG and/or gliadin and/or reticulin. We conclude that the tTG EIA compares well to both KS and PE IFAs when detecting IgA antibody against endomysium. We do not recommend the use of PE to detect EMA primarily because of the inconsistencies (i.e., tissue selection, quality, and preparation) and limited availability of commercially prepared PE tissue.