Abstract We demonstrated a new QIHC (Quantitative Immunohistochemistry) microfluidic PDMS (Polydimethylsiloxane) platform by the introduction of the aptamer specific to the Fc region of the IgG antibody as a reporting probe. The aptamer was designed and synthesized. Various breast cancer cell lines were prepared as paraffin block slides, which were covered by a microfluidic PDMS platform to form a micro-reaction chamber. Primary antibodies specific to marker proteins (HER2, ER, PR, and ki-67) for breast cancer characterization were loaded in the micro-fluidic chip prior to the introduction of the aptamer. A master mixture of QNASBA (Quantitative Nucleic Acid Sequence Based Amplification) was used to quantify marker proteins by real time amplification of the aptamers. The quantitative results of aptamer amplification were linearly proportional to the concentrations of 4 different primary antibodies. The characterization results of the aptamer-assisted IHC using the microfluidic platform were well-correlated with those of conventional IHC for breast cancer cell lines (SK-BR-3, MCF-7, MDA-MB-231). Objective quantitative evaluations were carried out and compared with conventional results for real clinical samples.