This paper aims to provide an overview and a critique of the methodologies and methods used in the research on sectarianism in the Middle East. The paper starts with a brief discussion on the distinction between methodology, method, and design. Then, it presents the predominant methodological approaches used in the research sectarianism. I then provide a critique of those approaches and argue that despite the growing number of quantitative and mixed-method studies, qualitative approaches still dominate the field. The paper concludes with a discussion on the challenges that scholars face when they conduct research in the Middle East and how those challenges impact on the type of the methodologyy and method the research adopts.