Imaging techniques play a crucial role in the modern era of medicine, particularly in gastroenterology. Nowadays, various non-invasive and invasive imaging modalities are being routinely employed to evaluate different gastrointestinal (GI) diseases. However, many instrumental as well as clinical issues are arising in the area of modern GI imaging. This minireview article aims to briefly overview the clinical issues and challenges encountered in imaging GI diseases while highlighting our experience in the field. We also summarize the advances in clinically available diagnostic methods for evaluating different diseases of the GI tract and demonstrate our experience in the area. In conclusion, almost all imaging techniques used in imaging GI diseases can also raise many challenges that necessitate careful consideration and profound expertise in this field.