Gastroenterology is the study of the gastrointestinal tract, which includes the esophagus, stomach, small and large intestines, liver, gall bladder and pancreas. Small, flexible scopes are used to perform esophagoscopy, gastroduodenoscopy, and colonoscopy. These procedures are a minimally invasive means to visualize the gastrointestinal tract and obtain biopsies. This can aid in the diagnosis of conditions such as inflammatory bowel disease, food allergies, gastrointestinal ulcers, or cancer. Additionally, these scopes are occasionally used to retrieve foreign bodies in the esophagus or stomach.

Respiratory medicine is the study of the upper respiratory tract (including the nose, nasopharynx, larynx, and trachea), and the lower respiratory tract (including the bronchi and lower airways) using radiographs and advanced imaging, including a CAT scan or MRI and rhinoscopy (using a scope), to visualize the nasal cavity, and sometimes obtain biopsies. A bronchoscope assesses the structure and function of the larynx, the trachea, and the lower airways. This can be useful in the diagnosis of common conditions such as collapsing trachea and laryngeal paralysis. Procedures such as an endotracheal wash or a bronchoalveolar lavage can be performed to examine cells from the lower airways and can be useful in the diagnosis of conditions such as canine chronic bronchitis, feline asthma, and pneumonia in both species.