Microsaccade research has recently reached a critical mass of studies that allows, for the first time, a comprehensive review of how microsaccadic dynamics change in neurological and ophthalmic disease. We discuss the various pathological conditions that affect microsaccades, their impact on microsaccadic and other fixational eye movement dynamics, and the incipient studies that point to microsaccadic features as potential indicators of differential and early diagnoses of multiple clinical conditions, from movement disorders to attention-deficit hyperactivity disorder to amblyopia. We propose that the objective assessment of fixational eye movement parameters may help refine differential diagnostics in neurological disease and assist in the evaluation of ongoing therapy regimes. In addition, determining the effects of ophthalmic disease on fixational eye movement features may help evaluate visual impairment in an objective manner, particularly in young patients or those experiencing communication difficulties.