This chapter describes several applications of causal discovery in biomedicine, in three different domains: medical, neuroimaging and gene regulation. In the medical domain, we present a method for modeling the Attention Deficit Hyperactivity Disorder (ADHD); and a work that investigates the causal risk factors for COVID-19. Then, we describe two approaches to recover brain effective connectivity from different modalities of neuro images. Lastly, we include two examples of causal discovery of gene regulatory networks, one based on observational data, and other that combines observational and interventional data.