Various biological and clinical applications require the quantification of the messenger RNA (mRNA) abundance of the biological materials under investigation. Reverse transcription-polymerase chain reaction (RT-PCR) is a popular technique for mRNA quantification. However, in these applications, multiple quantifications of mRNA are required from the same sample. Multiplex RT-PCR uses multiple primer pairs to amplify the specific targets simultaneously from a single sample. Therefore, multiplex RT-PCR is suitable for such applications. Complementary DNA (cDNA) microarray is a robust and versatile tool that allows researchers to examine the expression of hundreds or thousands of genes for the analysis of gene function, disease diagnosis, and drug discovery. Multiplex RT-PCR is usually performed for the cDNA preparation during the cDNA microarray experiments. Primer design is the most crucial step in multiplex RT-PCR. Therefore, the goal of this study was to implement an intelligent primer design system. The core of the system was based on mathematical techniques. The system can guide users to design cost effective primer collection. The system had also been successfully applied to two real world examples with biological and clinical significance.