We are currently witnessing a paradigm shift from evidence-based medicine to precision medicine, which has been made possible by the enormous development of technology. The advances in data mining algorithms will allow us to integrate trans-omics with clinical data, contributing to our understanding of pathological mechanisms and massively impacting on the clinical sciences. Cluster analysis is one of the main data mining techniques and allows for the exploration of data patterns that the human mind cannot capture. This chapter focuses on the cluster analysis of clinical data, using the statistical software, R. We outline the cluster analysis process, underlining some clinical data characteristics. Starting with the data preprocessing step, we then discuss the advantages and disadvantages of the most commonly used clustering algorithms and point to examples of their applications in clinical work. Finally, we briefly discuss how to perform validation of clusters. Throughout the chapter we highlight R packages suitable for each computational step of cluster analysis.