Aptamers have significant potential for use as imaging reagents as they can be isolated against cell-lines, tissue samples etc. and can be selected in such a way that they only bind to their intended target and not to related cells (or surrounding tissues). The ease with which aptamers can be site specifically labelled with a variety of fluorophores also facilitates their use in multiplexed analysis. Site specific labelling of aptamers means that all aptamers can be prepared in a functional conformation. This is in contrast to antibodies which are essentially labelled at random and may therefore be inactivated by the process.

Fluorescently labelled aptamers may be used to identify specific cells within a population by flow-cytometry and may also facilitate their purification by fluorescent activated cell sorting (FACS). They may also be used as cell / tissue specific imaging agents in techniques such as confocal microscopy.

Coupling of other imaging agents also allows aptamer binding to be detected by whole body imaging techniques such as magnetic resonance imaging (MRI).