Research into the genetic and physiological interactions of tumours with their host environment requires in vivo assays to address molecular expression patterns and function. In recent years much of this work has been performed using bioluminescent and fluorescent imaging techniques that allow real-time and non-invasive imaging of gene expression and (tumour) tissue development. Luminescence imaging has until now been more or less the only tool that allows the imaging of intra-osseous breast cancer cells and indeed this technique has been pioneered in our laboratory. Here we summarise some recent innovations and developments using cancer cells and some of the first imaging models of multimodal dual luminescence and luminescence combined with fluorescence of intra-osseous tumours. We further engineered our models to incorporate a specific insertion site in the genome and will discuss some of the possible applications. These include the insertion of signalling pathway-specific reporters and studying the fate of multiple injected populations in a single mouse. We conclude that recent improvements in luminescence- and fluorescence-detection platforms now clearly allow multimodal imaging which will greatly enhance our ability to assess gene function and for the first time to visualise multiple gene- and cellular interactions in real time and in vivo.