A method and apparatus for stabilizing the output of a mode-locked laser by monitoring the temporal behavior of the pulse train profile and controlling the laser cavity optical length and/or loss modulation frequency accordingly. A mismatch of the cavity optical length and the loss modulation frequency will yield a first characteristic noise condition on the laser beam pulse train when the optical length is too short for a given loss modulation frequency and a second, different noise condition when the optical length is too long. The laser beam is monitored and analyzed to determine which noise condition is present. The cavity optical length is adjusted accordingly by movement of one or more optical elements or by changing the index of refraction of one or more optical elements. In the alternative, or additionally, the loss modulation frequency can be adjusted to bring the laser back into mode lock.