Moyamoya disease (MMD) is an arteriopathy of the intracranial circulation predominantly affecting the branches of the internal carotid arteries. Heterogeneity in presentation, progression and response to therapy has prompted intense study to improve the diagnosis and prognosis of this disease. Recent progress in the development of moyamoya-related biomarkers has stimulated marked interest in this field. Biomarkers can be defined as biologically derived agents-such as specific molecules or unique patterns on imaging-that can identify the presence of disease or help to predict its course. This article reviews the current categories of biomarkers relevant to MMD-including proteins, cells and genes-along with potential limitations and applications for their use.