The horse, as a flight animal with a survival strategy involving rapid escape from predators, is a natural-born athlete with enormous functional plasticity of the respiratory system. Any respiratory dysfunction can cause a decline in ventilation and gas exchange. Therefore, respiratory diseases often lead to exercise intolerance and poor performance. This is one of the most frequent problems encountered by equine internists. Routine techniques used to evaluate respiratory tract diseases include clinical examination, endoscopic examination, radiographic and ultrasonographic imaging, cytological evaluation, and bacterial culture of respiratory secretions. New diagnostic challenges and the growing development of equine medicine has led to the implementation of advanced diagnostic techniques successfully used in human medicine. Among them, the use of computed tomography (CT) and magnetic resonance (MR) imaging significantly broadened the possibilities of anatomical imaging, especially in the diagnosis of upper respiratory tract diseases. Moreover, the implementation of spirometry, electrical impedance tomography (EIT), and impulse oscillation system (IOS) sheds new light on functional diagnostics of respiratory tract diseases, especially those affecting the lower part. Therefore, this review aimed to familiarize the clinicians with the advantages and disadvantages of the advanced diagnostic techniques of the equine respiratory tract and introduce their recent clinical applications in equine medicine.