Immunohistochemistry (IHC) is an indispensable method for the diagnosis of malignancy when alterations in tissue morphology remain deceptively subtle. IHC also demonstrates therapeutic significance by allowing for assessment of cell surface marker expression prior to commencement of immunotherapy. IHC can also provide prognostic indications through the detection of clinically relevant markers of tumourigenicity and invasiveness. For more than forty years, antibodies have demonstrated efficacy in chromogenic IHC. However, antibodies continue to harbour issues of batch-to-batch variability and cross-reactivity that are of detriment to the accuracy and precision of clinical histopathology. In contrast, aptamers are a relatively recent class of oligonucleotide-based, bio-recognition molecules, also known as ‘chemical antibodies.’ Aptamers are sequence-defined and synthesised entirely in vitro – virtually eliminating concerns of batch-to-batch variability, whilst providing ease of functionalisation through the ability to conjugate detection moieties at one, or many, pre-specified locations along their sequence. In addition, aptamers are around 10-20 times smaller than conventional antibodies. This may prove beneficial in detecting cells which co-express multiple surface markers of tumourigenicity. Currently, as a result of the large size of the antibody-chromogen complex, and the resulting potential for steric hindrance, no chromogenic, immunohistochemical double-staining systems are recommended for the detection of bio-markers which are co-localised within the same cellular compartment. Having previously generated aptamers against EpCAM and CD133 and demonstrated sensitive and specific chromogenic detection of these cancer stem cell markers in single-staining techniques, we tested their sensitivity in a chromogenic, sequential double-staining system in formalin-fixed paraffin-embedded colorectal carcinoma xenografts. We were able to demonstrate the detection of cells which co-express both markers at the cell surface. Parallel detection of two different stemness markers enhances the likelihood that co-expressing cells are cancer stem cells and also allows for the detection of single co-expressing cells that would prove highly difficult by the individual testing of serial tissue sections. The ability to sensitively detect co-localised bio-markers, without concerns over batch-to-batch variation, points to a promising future for aptamers in clinical histopathology.