Gastrointestinal T cells (GI-T) play a critical role in mucosal immunity, balancing tolerance and pathogen defence. T cells recognize antigens via T cell receptors (TCRs). Next-generation sequencing (NGS) is utilized to analyse TCR repertoires in contexts such as health, haematological diseases, autoimmunity, and inflammation. While some studies have explored T cell involvement in GI conditions, the integration of different techniques and examination of diverse tissues remain underdeveloped. In our “proof of concept” study, for the first time, we combined flow cytometry, TCR sequencing and transcriptomics to analyse T cell repertoires from bulk sorted T cells and from single cells. This combination provides information about both, specificity and functionality of particular T cells. We focused on biopsy samples from the stomach, colon, and compared these to blood samples from patients with and without inflammation associated with erosive gastritis. This combined approach allows unique insights into T cell biology. Through TCR clonotype analysis, we identified oligoclonal expansion in inflamed biopsies, with minimal TCR clonotype overlap between individuals, highlighting personalized immune responses. Gene expression analysis revealed upregulation of T cell activation and signalling and chemokines in inflamed biopsies. Single-cell sequencing provided deeper insights into specific T cell populations, identifying dominant clonotypes with cytotoxic function. Our findings underscore the importance of studying affected sites to fully understand T cell responses and localized immune reactions. Our approach opens unique possibilities for studying TCR and gene expression from limited biopsy material, potentially leading to personalized therapies and biomarkers for gastrointestinal diseases.