The Malmquist-Takenaka (MT) system is a complete orthonormal system in $H^2(T)$ generated by an arbitrary sequence of points in the unit disk that do not approach the boundary very fast. The nth point of the sequence is responsible for multiplying the nth and subsequent terms of the system by a Möbius transform taking the point to 0. One can recover the classical trigonometric system, its perturbations or conformal transformations, as particular examples of the MT system. However, for many interesting choices of the generating sequence, the MT system is less understood. We prove almost everywhere convergence of the MT series for three different classes of generating sequences.