We present and compare different numerical schemes for the integration of the variational equations of autonomous Hamiltonian systems whose kinetic energy is quadratic in the generalized momenta and whose potential is a function of the generalized positions. We apply these techniques to Hamiltonian systems of various degrees of freedom and investigate their efficiency in accurately reproducing well-known properties of chaos indicators such as the Lyapunov characteristic exponents and the generalized alignment indices. We find that the best numerical performance is exhibited by the "tangent map method," a scheme based on symplectic integration techniques which proves to be optimal in speed and accuracy. According to this method, a symplectic integrator is used to approximate the solution of the Hamilton equations of motion by the repeated action of a symplectic map S, while the corresponding tangent map TS is used for the integration of the variational equations. A simple and systematic technique to construct TS is also presented.