PURPOSE: Diagnosis of inflammatory bowel disease (IBD) involves history-taking and invasive procedures that primarily evaluate localized intestinal structures. Notably, glucagon-like peptide 1 (GLP-1) and its receptor (GLP-1R) have been established as potent participants in various inflammatory diseases. This study aimed to investigate the potential of molecular imaging targeting GLP-1R in the study of gastrointestinal physiology and disease. METHODS: Using dextran sulfate sodium (DSS)-induced IBD rats (n = 6), changes in GLP-1R expression in the gastrointestinal tract before and after DSS induction were determined by quantitative micro-PET/CT. Dynamic changes in GLP-1R expression after liraglutide treatment were also assessed in IBD rats. Transcription of GLP-1R and inflammatory factors in duodenal and colonic tissues were measured and subjected to correlation analysis. RESULTS: In normal rats, GLP-1R was highly concentrated in the proximal duodenum, with a higher distribution density near the distal end of the colonic segment. Proximal duodenal uptake of [(68)Ga]Ga-NOTA-MAL-Cys(39)-exendin-4 was significantly increased after DSS induction compared with controls. The increased colonic uptake closely correlated with the histopathologic score of epithelial injury. In IBD rats treated with liraglutide, proximal duodenal uptake was reduced. In addition, Western blotting and quantitative PCR confirmed changes in GLP-1R expression during disease progression. CONCLUSION: These findings underscore the role of molecular imaging in assessing dynamic changes in GLP-1R expression and its potential for improving diagnostic and therapeutic strategies for gastrointestinal disorders like IBD. It supports using Brunner's glands as a key site to observe GLP-1R expression, advancing research on the GLP-1R/GLP-1RA axis in complex gastrointestinal conditions.