We show that there is a manifestly covariant version of the Pauli Hamiltonian with equations of motion quadratic on spin and field strength. Relativistic covariance inevitably leads to noncommutative positions: classical brackets of the position variables are proportional to the spin. It is the spin-induced noncommutativity that is responsible for transforming the covariant Hamiltonian into the Pauli Hamiltonian, without any appeal to the Thomas precession formula. The Pauli theory can be thought to be 1/c 2 -approximation of the covariant theory written in special variables. These observations clarify the long standing question on the discrepancy between the covariant and Pauli Hamiltonians. We also discuss the transformational properties of spin axis in the passage from laboratory to comoving and instantaneous frames, and reveal the role of Thomas spin-vector in the covariant scheme.