Protein phosphorylation is known to play an important role in various cellular processes such as cell division, metabolism, survival and apoptosis. It is driven by specific enzymes, tyrosine and serine-threonine protein kinases. Human protein kinases constitute a complicated system with intricate internal and external interactions. The complexity and sophistication of the system implies its vulnerability. Alterations in functions of these enzymes may launch series of pathological changes within the cell and as a result cause diseases. Protein kinases have been shown to be involved in various pathological processes, first of all malignancies. Deregulation of different protein kinases has been found in chronic myelogenous leukaemia, gastrointestinal stromal tumours, various other sarcomas and cancers as well as non-malignant disorders. Therefore, they are regarded as important effectors in human pathology and represent prospective therapeutic targets.