One of the major lidar error sources not yet analyzed in the literature is the tolerance of the laser beam alignment with respect to the scanning mirror. In this paper, the problem of quantifying these errors is solved for rotating polygon mirror type lidar systems. An arbitrary deviation of the beam from its design direction-the vector of beam misalignment-can be described by two independent parameters. We choose these as horizontal and vertical components of the misalignment vector in the body frame. Either component affects both, horizontal and vertical lidar accuracy. Horizontal lidar errors appear as scan line distortions-along and across track shifts, rotations and scaling. It is shown that the horizontal component of misalignment results in a scan line first being shifted across the track and then rotated around the vertical at the new center of the scan line. Resulting vertical lidar error, being a linear function of the scan angle, is similar to that produced by a roll bias. The vertical component of the beam misalignment causes scan line scaling and an along track shift. The corresponding vertical error is quadratic with respect to the scan angle. The magnitude of these effects is significant even at tight alignment tolerances and cannot be realistically accounted for in the conventional calibration model, which includes only range, attitude and GPS biases. Therefore, in order to attain better accuracy, this model must be expanded to include the beam misalignment parameters as well. Addition of new parameters into the model raises a question of whether they can be reliably solved for. To give a positive answer to this question, a calibration method must utilize not only ground control information, which is typically very limited, but also the relative accuracy information from the overlapping flight lines.