SummaryNoninvasive in vivo fluorescence imaging of small animals as a method in preclinical research has developed considerably in recent years, and is used widely across a variety of disciplines such as oncology and infectious disease research. It provides a means of detecting a fluorescent signal within a living animal reflecting specific, mostly disease‐related, processes, such as parts of the host immune response, inflammation, cancer growth or presence of pathogens. As well as offering many advantages as a standalone technique, it can also be highly complementary to other imaging modalities. This review discusses aspects of light distribution in animal tissue and the implications on in vivo imaging; the most widely used imaging techniques including planar and tomographic imaging; advantages and challenges of the techniques; fluorescent contrast agents and some examples of applications. Rather than in detail reviewing studies using in vivo fluorescence imaging, we focus on the principles and practicalities of the method itself, so that the reader can apply these to their own research question.