Solid phases of visible fluorescence substance (VFS) of biological fluids (blood, urine, hemodialysate) which was proposed earlier as a morbidity and mortality marker by renal failure and diabetes were investigated in-depth by the methods of electron and confocal microscopy, optical spectroscopy and matrix assisted laser desorption-ionization (MALDI) mass spectroscopy. It is shown that dry VFS exists predominantly in the form of carbon–oxygen–nitrogen (N ≈ 8.7 wt. %) nanoparticles (NPs) (5 ≤ d ≤ 100 nm). For the first time the existence of the threshold energy Eg ≈ 2.15 eV for excitation of VFS was observed experimentally and confirmed by semi-empirical calculations of the bathochromic shift. A good accordance with the earlier autonomous theoretical calculations was achieved. Thus, the long wavelength limit (575 nm) of the spectral range where the VFS can be used as a fluorescent marker was reliably determined. A pilot MALDI comparative study of graphene oxide (GO) and urine VFS was carried out. Six kinds of nitrogenfree particles (412 ≤ M ≤ 456 Da) were observed in each substance and possible computer models of those have been composed. It is established that along with nitrogen-containing advanced glycation end products (AGEs) also nitrogen-free carbon–oxygen–hydrogen particles (probably toxic) with the composition and structure related to GO can exist in biofluids. Both types of particles should be taken into account in search for the reasons of high mortality among end stage renal disease patients.