A method for simultaneously amplifying at least two different target nucleic acid sequences contained in a sample comprising the steps of: (a) contacting a sample with at least two different amplification oligomer complexes and with at least two target capture oligomers, wherein a different amplification oligomer complex and a different target capture oligomer is provided for each of the at least two different target nucleic acid sequences, and wherein each of said amplification oligomer complexes comprises a first amplification oligomer member that is linked to a second amplification oligomer member; (b) providing conditions for hybridising said at least two amplification oligomer complexes and said at least two target capture oligomers to their respective different target nucleic acid sequences present in said sample and for hybridising said at least two target capture oligomers to a solid support and immobilized probe for performing a target capture step; (c) performing a washing step to remove unhybridised amplification oligomer complexes; (d) pre-amplifying said target nucleic acid sequences using said amplification oligomer complexes under isothermal amplification conditions, thereby generating a first amplification product for each target nucleic acid hybridized by an amplification oligomer complex; (e) splitting said pre-amplified sample into at least two separate secondary target specific amplification reactions; (f) in a secondary amplification, amplifying said pre-amplified sample under isothermal amplification conditions using target specific amplification oligomers, wherein universal amplification oligomers are not used in the secondary amplification, thereby generating second amplification products. (a) contacting a sample with at least two different amplification oligomer complexes and with at least two target capture oligomers, wherein a different amplification oligomer complex and a different target capture oligomer is provided for each of the at least two different target nucleic acid sequences, and wherein each of said amplification oligomer complexes comprises a first amplification oligomer member that is linked to a second amplification oligomer member; (b) providing conditions for hybridising said at least two amplification oligomer complexes and said at least two target capture oligomers to their respective different target nucleic acid sequences present in said sample and for hybridising said at least two target capture oligomers to a solid support and immobilized probe for performing a target capture step; (c) performing a washing step to remove unhybridised amplification oligomer complexes; (d) pre-amplifying said target nucleic acid sequences using said amplification oligomer complexes under isothermal amplification conditions, thereby generating a first amplification product for each target nucleic acid hybridized by an amplification oligomer complex; (e) splitting said pre-amplified sample into at least two separate secondary target specific amplification reactions; (f) in a secondary amplification, amplifying said pre-amplified sample under isothermal amplification conditions using target specific amplification oligomers, wherein universal amplification oligomers are not used in the secondary amplification, thereby generating second amplification products.