Abstract: Compositions and methods are disclosed for detecting multiple target analytes, particularly polynucleotide target analytes. In accordance with one aspect of the invention, a template-dependent extension reaction is performed to generate detection probes, such that each detection probe has (i) at least one molecular tag attached by a cleavable linkage and (ii) either a capture moiety or a cleavage-inducing moiety attached. The template-dependent extension reaction may be carried out directly on a polynucleotide analyte to generate molecular tags, wherein the polynucleotide analyte serves as a template in the template-dependent extension reaction, or it may be carried out indirectly on an oligonucleotide label that, in turn, is attached to a binding moiety specific for an analyte of interest. In either case, a plurality of molecular tags are generated, after which they are separated and identified to determine the presence or absence or the quantity of the target analytes in a sample.