Intratumoral heterogeneity has become the main obstacle in treatment of malignant diseases. Although it has been known for decades, that within a single tumor there are sub-populations of tumor cells that are significantly different, the interest in this issue has for long been weak. However, with the emergence of the need for a more detailed analysis of tumor properties, interest for this area is again raising. Since it has become clear that intratumoral heterogeneity is one of the main reasons of tumor resistance and development of more aggressive metastases, it is essential to integrate and extend knowledge to sufficiently elucidate this fact. New light has been shed on significance of discovering new methods for determining intratumor heterogeneity which should help presume cancer progression including invasion, metastasis, drug resistance and disease relaps and according to that administration of the right treatment. Despite the fact that there are more and more evidence of intratumoral heterogeneity in different tumors, its origin have not been confirmed, and are still not clear. So far there are two theories that try to elucidate the origin of intratumor heterogeneity: the idea of „cancer stem cells“ and the idea of ongoing mutations that form different cell clones. Although presented in the literature as mutually restricted hhypothesis, they both play an essential role in the generation of heterogenity.