Aptamers are single stranded oligonucleotides that fold into three dimensional structures and are able to recognize a variety of molecular targets. Due to the similarity to antibodies with regards to specificity and affinity and their chemical versatility, aptamers are increasingly used to create targeted probes for in vivo molecular imaging and therapy. Hence, aptamer-based probes have been utilized in practically all major imaging modalities such as nuclear imaging, magnetic resonance imaging, x-ray computed tomography, echography and fluorescence imaging, as well as newer modalities such as surface enhanced Raman spectroscopy. Aside from targeting, aptamers have been used for the creation of sensors that allow the localized detection of cellular markers such as ATP in vivo. This review focuses on in vivo studies of aptamer-based probes for imaging and theranostics since the comprehensive overview by Bouvier-Müller and Ducongé in 2018.