Most horses affected by headshaking (HS) are diagnosed with idiopathic trigeminal-mediated headshaking (i-TMHS) when no underlying disease is found. Diagnosis is made by the exclusion of differentials considering history, clinical signs, and diagnostic investigations. Therefore, in horses presented with headshaking, many diagnostic procedures and therapies are conducted. Retrospectively, the digital patient records of 240 horses with HS were analysed regarding the impact of diagnostic procedures on diagnosis, therapy, and outcome. Horses were extensively examined using a standardised protocol including clinical (ophthalmologic, orthopaedic, neurologic, dental) examination, blood analysis, and imaging techniques (endoscopy, radiographs, computed tomography (CT), and magnetic resonance imaging). Many findings were revealed but were of clinical relevance in only 6% of the horses. These horses were, therefore, diagnosed with secondary headshaking (s-HS). In addition, all of these horses demonstrated a positive outcome. The CT of the head revealed 9/10 of the clinically relevant findings. Other diagnostic procedures had no major additional impact. Conclusively, the diagnostic investigation of horses with HS should aim at differentiating i-TMHS from s-HS. The clinical relevance of findings should be verified through diagnostic anaesthesia or targeted therapy depending on risks, invasiveness, and expected benefits. To reduce the multitude of examinations, diagnostic investigations should focus on the CT of the head in those horses with suspicion of i-TMHS based on typical history, clinical signs, and physical examination.