We describe a connection between the subjects of cluster algebras, polynomial identity algebras and discriminants. For this, we define the notion of root of unity quantum cluster algebras and prove that they are polynomial identity algebras. Inside each such algebra we construct a (large) canonical central subalgebra, which can be viewed as a far reaching generalization of the central subalgebras of big quantum groups constructed by De Concini, Kac and Procesi and used in representation theory. Each such central subalgebra is proved to be isomorphic to the underlying classical cluster algebra of geometric type. When the root of unity quantum cluster algebra is free over its central subalgebra, we prove that the discriminant of the pair is a product of powers of the frozen variables times an integer. An extension of this result is also proved for the discriminants of all subalgebras generated by the cluster variables of nerves in the exchange graph. These results can be used for the effective computation of discriminants. As an application we prove an explicit formula for the discriminant of the integral form over ${\mathbb{Z}}[\varepsilon]$ of each quantum unipotent cells of De Concini, Kac and Procesi for arbitrary symmetrizable Kac-Moody algebras, where $\varepsilon$ is a root of unity.