The monoclonal antibody against the AC133 epitope of CD133 has been widely used as a cell surface marker of cancer stem cells in several different cancer types. Here, we describe the isolation and characterisation of two RNA aptamers, including the smallest described 15 nucleotide RNA aptamer, which specifically recognise the AC133 epitope and the CD133 protein with high sensitivity. As well, both these aptamers show superior tumour penetration and retention when compared to the AC133 antibody in a 3-D tumour sphere model. These novel CD133 aptamers will aid future development of cancer stem cell targeted therapeutics and molecular imaging. © 2012.