Systemically injected drug delivery systems distribute into various organs and tissues, including liver, spleen and kidneys. Recent reports pointed out a significant accumulation of systemically injected nanoparticles in the skin. Skin constitutes the largest organ in the body with important immune functions, and accumulation of drug delivery systems could have significant implications for skin toxicity in living subjects. Fiber optic-based near-infrared spectroscopy (FONIRS) setup was developed and tested for measuring of NIR (760 nm excitation) emission spectra in the skin. Ex vivo spectral measurements of NIR fluorescence through the skin showed linear response down to 34 femtomole of dye DiR. Following systemic injection of IRDye 800 labeled 500 kDa dextran, FONIRS detected an immediate and stable accumulation of fluorescence in the skin. Longitudinal monitoring of skin accumulation and elimination of IRDye 800-labeled therapeutic anti-epidermal growth factor antibody (cetuximab) showed significant signal in the skin after the antibody cleared from circulation. Comparison of skin accumulation of DiR labeled, long-circulating PEGylated liposomes with short-circulating non-PEGylated liposomes showed much higher accumulation of PEGylated liposomes that persisted several days after the liposomes cleared from blood. Measurements with FONIRS enabled to estimate skin concentration of liposomes (percent of injected dose per gram). This simple and practical approach can be used to monitor accumulation of drug delivery systems in preclinical and clinical studies.