In a method and apparatus for synchronizing the receiver and the emitter in an autocompensating quantum cryptography system it is allowed to one of the stations (for example the emitter) to define the timing of all its operations (for example the application of a signal onto the modulator used to encode the values of the bits) as a function of a time reference. This time reference can either be transmitted using a channel from the other station (for example the receiver). It can also consist of a time reference synchronized with that of the other station through using information transmitted along a channel and a synchronization unit. Preferably a time reference unit is provided at each station. One of these time reference units functions as a master, while the other one function as a slave. The slave is synchronized with the master using information transmitted over a communication channel by a synchronization unit.