Expression profiling of biological samples using microarray technologies has proven to be a powerful tool for molecular classification and biomarker identification. Visualization of similarities between biological samples from their molecular signatures is essential in forming new hypotheses. Multidimensional scaling is one of the methods that converts the structure in the similarity matrix to a simple geometrical picture: the larger the dissimilarity between two samples (evaluated through gene expression profiling), the further apart the points representing the experiments in the picture should be. In this unit, we will discuss the mathematical fundamentals of this method, along with step‐by‐step procedures that allow users to quickly obtain the results, provided that all necessary resources are ready. Examples of applying the MDS program and the interpretation of these results are also provided in this unit