The invention relates to improved methods of amplifying and optionally quantifying and/or identifying a plurality of selected nucleic acid molecules from a pool of nucleic acid molecules. A first round of multiplex amplification used where the amplification reaction is allowed to proceed to a point prior to that at which significant competition between amplicons for reaction components has occurred. This is the followed by a second round of amplification that typically includes a fluorescent reporter to allow for each of the selected nucleic acid sequences to be quantified. The methods are useful for the amplification and quantification of nucleic acids from a variety of sources, such as gene expression products, whereby many such products may be amplified and quantified from very limited samples and from degraded archival samples.