This document provides guidelines for writing a research protocol for a MD thesis in paediatric medicine at the Institute of Medicine in Nepal. It recommends including a 1-page synopsis with rationale, objectives, methods, and expected results. The protocol should also describe the rationale and background literature, objectives and hypotheses, experimental design including subjects and inclusion/exclusion criteria, number of subjects, analysis methods, materials and methods, study duration and center, budget, and references. Following these guidelines will help MD students to develop their thesis protocol and smoothly start their research work.