Abstract: A method based on polymerase chain reaction (PCR) amplification and oligonucleotide ligase assay (OLA) reaction is provided for analyzing complex genetic systems in a single reaction vessel. The method involves simultaneously incubating a sample containing one or more target polynucleotides with PCR primers and OLA probes in a single reaction mixture. The presence of variant polynucleotide sequences in the sample is determined by detecting and identifying the products of the OLA reaction.