The establishment of a single validated endoscopic laryngeal grading system for assessing recurrent laryngeal neuropathy (RLN) is desirable to facilitate direct comparisons between the findings of different clinical and research groups worldwide. The objective of this study was to assess the relationship between the Havemeyer endoscopic laryngeal grading system and histopathological changes consistent with RLN in the left cricoarytenoideus dorsalis (CAD) muscle of horses of different breeds with a full range of clinical severities of RLN, i.e., from normal endoscopic laryngeal function to complete laryngeal hemiplegia. Endoscopic grading of laryngeal function of 22 horses was performed using the Havemeyer endoscopic laryngeal grading system. A biopsy sample of the left CAD muscle was obtained from each horse, either at post mortem examination (n = 16), or during routine laryngoplasty surgery (n = 6). A semi-quantitative histopathological scoring system was used to grade the severity of histopathological lesions consistent with RLN in the left CAD muscle of each horse. A significant positive correlation (rs = 0.705, p < 0.001) was found between the Havemeyer grades and sub-grades of laryngeal function and the semi-quantitative assessment of histopathological lesions consistent with RLN in the left CAD muscle. However, a wide spread of muscle histopathological scores was obtained, particularly from horses with Havemeyer sub-grades II.1, III.1 and III.2. In conclusion, the Havemeyer endoscopic laryngeal grading system was found to broadly correlate with histopathological changes consistent with RLN in equine cricoarytenoideus dorsalis muscle.