Equine 4th and 6th branchial arch defects are not uncommon in the equine population at large but can be challenging to diagnose and treat. An understanding of the anatomical structures that can be involved and how structural abnormalities may affect laryngeal function is important for clinicians faced with such cases. Diagnosis is often made using resting endoscopic examination alone but, in many cases, laryngeal ultrasound, radiography and 3-dimensional (3D) imaging techniques can be useful in confirming a diagnosis and for detecting which structures are abnormal. Exercising endoscopy is an important tool when ascertaining whether treatment is an option, for guiding treatment choice and making a prognosis for athletic function.