Molecular imaging plays an increasingly powerful role in elucidating pathophysiological pathways, in advancing drug discovery and in deciphering developmental processes. Multiple modalities, including optical imaging, ultrasound, nuclear imaging, computed tomography and various techniques of MRI are now being used to obtain fundamental new insights at the cellular and molecular level, both in basic research, using animal models and in clinical studies. In permitting unique optical access, the eye is particularly well suited for molecular imaging, for example, transgenic mice in which the fractalkine receptor is rendered intrinsically fluorescent to allow for in vivo monitoring of myeloid immune cells within the retina and choroid by scanning laser ophthalmoscopy (SLO). Retinal cell apoptosis can be assessed by intravitreal injection of fluorescent-labelled annexin 5 in vivo using a similar SLO technique. Intravital microscopy also allows visualisation of CD11c-positive dendritic cells in transgenic mice expressing yellow-fluorescent protein in these immune cells. Adoptive transfer of fluorescent-labelled transgenic T-cells enables visualisation of infiltration by specific T-cells into various eye compartments. On the other hand, functional imaging can be provided by new MR methodologies: deuterium MRI and diffusion MRI analysis techniques permit dynamic studies of water movement in animal eyes. MRI also enables pharmacokinetic studies on ocular drug delivery and detects biomarkers for treatment efficacy in retinopathies. Undoubtedly, these and further molecular imaging techniques currently being developed will have a fundamental impact on experimental and clinical ophthalmology and thus on our understanding of eye disease and development of therapy in general.