Delivery of upconversion microparticles [Y2O3:Yb, Er] and quantum dots (CuInS2/ZnS coated with PEG-based amphiphilic polymer) into rat skin using the fractional laser microablation has been studied in vivo. Luminescence spectroscopy, optical coherence tomography, confocal microscopy, and histochemical analysis were used for visualization of nanoparticles in microchannels. Results have shown that the upconversion microparticles are detected more efficiently in comparison with the quantum dots. The fluorescence intensity of the inserted upconversion microparticles is higher, when the Omnipaque™ was applied as a skin optical clearing agent. The fluorescent images of upconversion nanoparticle distribution indicate the advantage of particle delivery into skin by ultrasound.