Comparative size and structure characterization of silver and selenium nanoparticles obtained and stabilized in different polymer solutions was performed by transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS). Effects of instrumental properties, nature of the samples, data collecting and data processing on accuracy of measurements are highlighted and summarized. Numerical differences in the mode diameter values derived from the TEM and SAXS data were found to have different sources. The SAXS results can be misleading in case of small particles (2-4 nm), for instance, Ag nanoparticles formed and stabilized in some aqueous polymer solutions due to instrumental limits, while TEM can provide sufficient statistics on such nanoparticles. SAXS is efficient in characterization of size distributions for soft Se-polymer composite particles of 20 to 100 nm in diameter. TEM is mandatory for investigating the chemical and phase composition of particles in mixtures, and their formation mechanism.