Abstract: The present invention provides methods and kits for conducting multiplex nucleic acid amplification reactions by controlling target sequence replication times. In one aspect, such control is exerted by selecting different lengths of target polynucleotides for amplification. In another aspect, control is exerted by providing sequence-specific polymerase inhibitors, such as specific blocking oligonucleotides. In accordance with the invention, multiple target polynucleotides can be sequentially amplified in an amplification reaction conducted in different stages, wherein amplification of sequences with longer replication times is permitted in one stage but precluded in other stages by modifying polymerase extension times in the course of the reaction.