The amygdala is a subcortical structure located bilaterally in the medial temporal lobes. This structure captures the attention of neuroscientists due to its role in emotion processing and learning. Animal studies indicate that groups of nuclei situated in different parts of the amygdala are components of distinct neural circuits underlying in a varied way emotional and cognitive processes. Some authors even argue that the amygdala is deemed a single unit only owing to nuclei groups located closely. Verifying such a hypothesis with regard to humans is very difficult as, until quite recently, there has been only one method of amygdala parcellation, based on post-mortem anatomical tissue analysis. However, in more recent years, several attempts have been made to parcellate the human amygdala on the basis of structural and functional connectivity with other areas of the brain using magnetic resonance imaging techniques. Results of analyses conducted until now are not congruent in respect of the number and localisation of the obtained amygdala parts. This may be a consequence of using different techniques (functional magnetic resonance imaging or diffusion tensor imaging), various acquisition parameters of scanner and distinct data analysis procedures, especially clustering algorithms. Future research should be focused on the development of the most reliable method for parcellation of the human amygdala to enable clear identification. This will allow one to learn more about the functional organisation of this structure in humans.