Recent years have seen intense appreciation for the heterogeneous and dynamic nature of solid tumours. Consequently, the field of therapeutic oncology has seen a swift evolution away from a ‘one-size-fits-all’ approach, toward the relatively tailor-made approach that is precision oncology. However, in order to realise the full potential of individualised treatment strategies, there is urgent need for sensitive, specific and precise methods of sampling tumour heterogeneity at the molecular level. Aptamers are small, single-stranded oligonucleotides which fold to form complex tertiary conformations as a result of intra-nucleotide binding. Aptamers are colloquially known as ‘chemical antibodies’ because they specifically bind their targets via an induced-fit mechanism, in a similar manner to their conventional protein counterparts. Aptamers represent a promising alternative to traditional antibodies due to their relatively small size, ease of functionalisation and minimal batch-to-batch variability. Furthermore, the ability to easily functionalise aptamers with reporter moieties in a 1:1 stoichiometric ratio confers greater benefits over traditional antibodies in terms of accurate diagnostic quantitation. Using aptamers against the cancer stem cell-associated membrane proteins, EpCAM and CD133, we utilised ‘aptahistochemistry’ to identify this highly invasive subpopulation of tumour cells by a chromogenic, sequential double-staining technique in FFPE colorectal carcinoma xenografts. Due to the potential for steric hindrance, similar techniques utilising antibodies are not recommended for targets which are co-localised within the same cellular compartment. Having demonstrated the utility of our aptamers in discerning intratumoural heterogeneity in solid tissues, we then turned our attention towards less invasive ‘liquid biopsy’ methods for the detection and characterisation of circulating tumour cells. We have designed several capillary-driven, 3D-printed microfluidic chips. The droplet-based diagnostic chips produce a chromogenic result, which can be read by the unaided eye in under 10 minutes and has the potential for removal of viable cells for further downstream analysis or possible ex-vivo cell culture. This would allow for relatively non-invasive, real-time monitoring of disease progression and treatment responses for effective, personalised treatment stratification.