Optical coherence tomography (OCT) is an emerging medical imaging technology that can generate high resolution cross-sectional imaging (1–2 mm in depth) of tissue microstructure in situ and in real time. Fluorescence imaging provides tissue biochemical, metabolism, and molecular information by measuring fluorescence intensity or spectroscopy of either intrinsic fluorophores or exogenous contrast agents. The combination of these two modalities provides complementary morphological, functional and molecular information to comprehensively assess tissue status. There is a great interest to further extend the fluorescence imaging into tomography in order to provide depth-resolved molecular function that can be coregistered with 3-D tissue morphology provided by OCT. In this paper, we present a combined OCT and line-scanning fluorescence laminar optical tomography (FLOT) system for simultaneous 3-D morphological and molecular imaging with 10–100 µm resolution and millimeter-scale imaging depth. Co-registration on a capillary phantom with fluorescence dye Cy5.5 using the system has been demonstrated.