Optical molecular imaging in small animals harnesses the power of highly specific and biocompatible contrast agents for drug development and disease research 1-7 . However, the widespread adoption of in vivo optical imaging has been inhibited by its inability to clearly resolve and identify targeted internal organs. Optical tomography 8-11 and combined X-ray and micro-computed tomography (micro-CT) 12 approaches developed to address this problem are generally expensive, complex or incapable of true anatomical co-registration. Here, we present a remarkably simple all-optical method that can generate co-registered anatomical maps of a mouse's internal organs, while also acquiring in vivo molecular imaging data. The technique uses a time series of images acquired after injection of an inert dye. Differences in the dye's in vivo biodistribution dynamics allow precise delineation and identification of major organs. Such co-registered anatomical maps permit longitudinal organ identification irrespective of repositioning or weight gain, thereby promising greatly improved accuracy and versatility for studies of orthotopic disease, diagnostics and therapies.Accurate optical molecular imaging of the internal organs of small animals could revolutionize in vivo drug and disease research 1-7 . Yet, for non-invasive in vivo optical imaging, the effects of intrinsic absorption and scattering distort and attenuate signals from any target deeper than a few millimetres. This makes the study of in situ orthotopic tumours or diseased organs highly challenging. Further, because targeted fluorescent 9 and bioluminescent 13 molecular probes are designed to label only targeted cells, typical images do not reveal adjacent or landmark organs that could aid in identification of a targeted organ. Autofluorescence and nonspecific labelling further confound interpretation 14 . Superficial subcutaneous xenografts are much simpler to measure, but often do not resemble the human disease; for example, transplanted cancer-cell xenograft tumours are often surrounded by a pseudocapsule, have limited chances to invade major anatomical structures and rarely spread metastasis 15,16 .These difficulties have motivated the development of complex tomographic approaches and multimodality imaging systems that are generally expensive, complex and often inaccurate.