In this paper we discuss trigger signals synchronisation and trigger input alignment in the ALICE trigger system. The synchronisation procedure adjusts the phase of the input signals with respect to the local Bunch Crossing (BC) clock and, indirectly, with respect to the LHC bunch crossing instant. The synchronisation delays are within one clock period: 0-25 ns. The alignment assures that the trigger signals originating from the same bunch crossing reach the processor logic in the same clock cycle. It is achieved by delaying signals by an appropriate number of full clock periods. We propose a procedure which will allow us to find alignment delays during the system configuration, and to monitor them during the data taking.