This paper presents a novel minimally invasive MEMS (micro-electromechanical system)-based micro-biopsy catheter for the diagnosis of gastrointestinal tissue samples. Conventional macro-scale biopsy tools such as biopsy forceps often cause a significant discomfort, infectious risk, and injury to the patients. In this study, a disposable micro-scale biopsy tool is proposed for the first time and MEMS technology is implemented for the fabrication process. Micro-biopsy catheter successfully extracts tissue samples from the small intestines of the anesthetized rabbit and pig. The proposed micro biopsy catheter is found to be useful in minimally invasive diagnosis.