This chapter presents expected applications of molecular layer deposition (MLD) to biomedical photonics. Liquid-phase MLD is expected to be a powerful process in cancer therapy. Liquid-phase MLD is suitable for constructing the photosensitizers for two-photon absorption. The liquid-phase MLD can construct molecular structures by stacking molecules with designated sequencies. This can be regarded as a kind of in-situ syntheses within human bodies. An Reflective Self-organizing lightwave network (R-SOLNET) is constructed to connect the optical fiber and the cancer cells. By introducing surgical laser beams into the SOLNET, cancer cells are destroyed. In integrated photoluminescence analysis chips, microfluidic circuits that contain emissive materials are inserted between two optical waveguide films. Molecular recognition chips consist of molecule-sensitive waveguides. By setting an array of optical circuits with embedded wavelength filters for different wavelengths, spectral analysis of integrated photoluminescence can be performed for many kinds of materials at one time.