The excellent optical properties of quantum dots (QDs), such as high brightness, high photostability, continuous absorption, and narrow emission bandwidth, make them ideal as optical labels to develop QD-based immunohistofluorescence (IHF) imaging for multiplexing cancer biomarker detection on formalin-fixed and paraffin-embedded (FFPE) tissues. IHF is very important for the prediction of a patient's response to cancer chemotherapy or radiotherapy. QD-based IHF faces several challenges that differ from those encountered by organic dye based IHF for clinical assays. The current work addresses some of these issues. Initially, the chemical stability of QDs and organic dyes were compared. The results showed that QDs were stable for at least 5 months on FFPE tissue, whereas organic dyes were photobleached shortly after exposure to light. Various staining methods were also studied. QD fluorescence intensity on the tissue stained with primary antibody (Ab, p16, survivin, EF1α) conjugated QDs from our company was comparable to the signal from a commercially available method in which the tissue was stained with a primary p16 Ab and a QD-labeled secondary goat anti mouse Ab respectively. Finally, the effect of the amount of Ab conjugated to QD on tissue imaging was also studied. There was no significant increase in the QD fluorescence signal on tissues when the Ab:QD ratio increased from 5 to 30. In addition, protein G was tested as an adaptor protein to link Ab to QDs for IHF staining. However, the proper blocking of the protein G on QDs was necessary to reduce crosstalk. The biomarker quantification in QD-based IHF was validated by conventional Western blot and immunohistochemistry. The results contained herein demonstrate a promising application of QDs in multiplex detection and quantification of biomarkers.