This study compares the initial and post-treatment diagnosis of 85 patients with minor structural alterations of the vocal fold cover (MSAVFC), defined as subtle deviations from normal laryngeal anatomy. MSAVFC may occur independently or in association with lesions of the vocal folds, and may be difficult to diagnose in either case. The intent of the study was to examine factors contributing to difficulties in diagnosis. Results indicated that leukoplakia, chronic laryngitis, polyp, contralateral nodular reaction, edema, vocal nodules, and unilateral vocal fold inflammation were often associated with MSAVFC, and often obscured its diagnosis. Leukoplakia was the most common associated lesion that co-occurred with MSAVFC. Sulcus vocalis type pocket was the most common MSAVFC and was often interpreted as another type of MSAVFC or misdiagnosed as an associated lesion.