Method of performing a specific transcription-based amplification reaction of a selected first target nucleic acid in a sample, in a reaction wherein reagents specific for amplification of more than one target nucleic acid are present, comprising contacting the sample with at least a first oligonucleotide pair for amplifying a first target nucleic acid and a second oligonucleotide pair for amplifying a second nucleic acid target (a) the first oligonucleotide pair consisting of a first promoter oligonucleotide having a 5' end and a 3' end and being non-blocked, the first promoter oligonucleotide comprising, at the 5' end, an RNA polymerase promoter sequence, and 3' of the RNA polymerase promoter sequence, a sequence complementary to a first target portion of the first target nucleic acid and a first primer oligonucleotide that is not blocked comprising a sequence homologous to a second target portion of the first target nucleic acid, which second target portion is 5' of the first target portion of the first target nucleic acid, and (b) a second oligonucleotide pair consisting of a second promoter oligonucleotide having a 5' end and a 3' end, the second promoter oligonucleotide comprising, at the 5' end, an RNA polymerase promoter sequence, and 3' of the RNA polymerase promoter sequence, a sequence complementary to a first target portion of a second target nucleic acid wherein further, the second promoter oligonucleotide comprises, at the 3' end, a blocking moiety such that extension therefrom is essentially prohibited and a second primer oligonucleotide that is not blocked comprising a sequence homologous to a second target portion of the second target nucleic acid, which second target portion is 5' of the first target portion of the second target nucleic acid, and providing selected reagents and conditions for transcription-based amplification, and amplifying the nucleic acid targets, thereby performing a specific transcription-based amplification reaction of a selected first target nucleic acid in a sample, in a reaction wherein reagents specific for amplification of more than one target nucleic acid are present, and wherein the first target is less preferentially amplified. contacting the sample with at least a first oligonucleotide pair for amplifying a first target nucleic acid and a second oligonucleotide pair for amplifying a second nucleic acid target (a) the first oligonucleotide pair consisting of a first promoter oligonucleotide having a 5' end and a 3' end and being non-blocked, the first promoter oligonucleotide comprising, at the 5' end, an RNA polymerase promoter sequence, and 3' of the RNA polymerase promoter sequence, a sequence complementary to a first target portion of the first target nucleic acid and a first primer oligonucleotide that is not blocked comprising a sequence homologous to a second target portion of the first target nucleic acid, which second target portion is 5' of the first target portion of the first target nucleic acid, and (b) a second oligonucleotide pair consisting of a second promoter oligonucleotide having a 5' end and a 3' end, the second promoter oligonucleotide comprising, at the 5' end, an RNA polymerase promoter sequence, and 3' of the RNA polymerase promoter sequence, a sequence complementary to a first target portion of a second target nucleic acid wherein further, the second promoter oligonucleotide comprises, at the 3' end, a blocking moiety such that extension therefrom is essentially prohibited and a second primer oligonucleotide that is not blocked comprising a sequence homologous to a second target portion of the second target nucleic acid, which second target portion is 5' of the first target portion of the second target nucleic acid, and (a) the first oligonucleotide pair consisting of a first promoter oligonucleotide having a 5' end and a 3' end and being non-blocked, the first promoter oligonucleotide comprising, at the 5' end, an RNA polymerase promoter sequence, and 3' of the RNA polymerase promoter sequence, a sequence complementary to a first target portion of the first target nucleic acid and a first primer oligonucleotide that is not blocked comprising a sequence homologous to a second target portion of the first target nucleic acid, which second target portion is 5' of the first target portion of the first target nucleic acid, and (b) a second oligonucleotide pair consisting of a second promoter oligonucleotide having a 5' end and a 3' end, the second promoter oligonucleotide comprising, at the 5' end, an RNA polymerase promoter sequence, and 3' of the RNA polymerase promoter sequence, a sequence complementary to a first target portion of a second target nucleic acid wherein further, the second promoter oligonucleotide comprises, at the 3' end, a blocking moiety such that extension therefrom is essentially prohibited and a second primer oligonucleotide that is not blocked comprising a sequence homologous to a second target portion of the second target nucleic acid, which second target portion is 5' of the first target portion of the second target nucleic acid, and providing selected reagents and conditions for transcription-based amplification, and amplifying the nucleic acid targets, thereby performing a specific transcription-based amplification reaction of a selected first target nucleic acid in a sample, in a reaction wherein reagents specific for amplification of more than one target nucleic acid are present, and wherein the first target is less preferentially amplified.