Multiphoton microscopy (MPM) of a dually fluorescence-labeled model system in excised human skin is employed for high-resolution three-dimensional (3D) visualization in order to study the release, accumulation, and penetration properties of drugs released from nanoscale carrier particles in dermal administration. Polymer particles were covalently labeled with fluorescein, whereas Texas Red as a drug-model was dissolved in the particles to be released to the formulation matrix. Single nanoparticles on skin could easily be localized and imaged with diffraction-limited resolution. The temporal evolution of the fluorescent drug-model concentration in various skin compartments over more than 5 hours was investigated by multiphoton spectral imaging of the same area of the specimen. The 3D penetration profile of the drug model in correlation with skin morphology and particle localization information is obtained by multiple laser line excitation experiments. MPM combined with spectral imaging was found to allow noninvasive long-term studies of particle-borne drug-model penetration into skin with subcellular resolution. By dual color labeling, a clear discrimination between particle-bound and released drug model was possible. The introduced technique was shown to be a powerful tool in revealing the dermal penetration properties and pathways of drugs and nanoscale drug vehicles on microscopic level.