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We suggest that the structure factor could be a source of uncertainty when the number concentration of non-absorbing aggregate particles is experimentally determined from Rayleigh–Debye–Gans (RDG) scattering theory. Different characteristics of various structure factors have been examined as a function of qRg. We present deviation of various structure factors from the exponential structure factor. Number concentrations estimated from various structure factors differ in the range of 1.0 < qRg < 10 where most of flame-synthesized non-absorbing particles are present as aggregates. We compare aggregate number concentrations of silica particles determined using various structure factors.