A simple and reliable PCR-based method to quantitate gene expression is described. Following the digestion of double-stranded cDNA by a restriction enzyme, an adaptor is ligated to a cDNA from a first RNA sample, and another adaptor to a second RNA sample. The two adaptors share a common sequence at the outer region, but differ in size. Equal amounts of the ligated samples are mixed, and amplified by an adaptor-primer and a primer specific to the gene of interest. Products derived from the two sources differ in size, and can be separated by denaturing polyacrylamide gel electrophoresis. The ratio of the two products reveals the relative level of gene expression. Since the technique avoids the need to construct internal standards, it is especially useful for the analysis of many different gene transcripts.