In this paper we study properties of Lax and transfer matrices associated with quantum integrable systems. Our point of view stems from the fact that their elements satisfy special commutation properties, considered by Yu I Manin some 20 years ago at the beginning of quantum group theory. These are the commutation properties of matrix elements of linear homomorphisms between polynomial rings; more explicitly these read: (1) elements of the same column commute; (2) commutators of the cross terms are equal: [Mij, Mkl] = [Mkj, Mil] (e.g. [M11, M22] = [M21, M12]). The main aim of this paper is twofold: on the one hand we observe and prove that such matrices (which we call Manin matrices in short) behave almost as well as matrices with commutative elements. Namely, the theorems of linear algebra (e.g., a natural definition of the determinant, the Cayley–Hamilton theorem, the Newton identities and so on and so forth) have a straightforward counterpart in the case of Manin matrices. On the other hand, we remark that such matrices are somewhat ubiquitous in the theory of quantum integrability. For instance, Manin matrices (and their q-analogs) include matrices satisfying the Yang–Baxter relation ‘RTT=TTR’ and the so-called Cartier–Foata matrices. Also, they enter Talalaev's remarkable formulae: for the ‘quantum spectral curve’, and appear in the separation of variables problem and Capelli identities. We show that theorems of linear algebra, after being established for such matrices, have various applications to quantum integrable systems and Lie algebras, e.g. in the construction of new generators in (and, in general, in the construction of quantum conservation laws), in the Knizhnik–Zamolodchikov equation, and in the problem of Wick ordering. We propose, in the appendix, a construction of quantum separated variables for the XXX-Heisenberg system.