The size, surface charge and agglomeration state of nanoparticles under physiological conditions are fundamental parameters to be determined prior to their application in toxicological studies. Although silica-based materials are among the most promising candidates for biomedical applications, more systematic studies concerning the characterisation before performing toxicological studies are necessary. This interest is based on the necessity to elucidate the mechanisms affecting its toxicity. We present here TEM, SAXS and SMPS as a combination of methods allowing an accurate determination of single nanoparticle sizes. For the commercial material, Ludox TM50 single particle sizes around 30 nm were found in solution. DLS measurements of single particles are rather affected by polydispersity and particles concentration but this technique is useful to monitor their agglomeration state. Here, the influence of nanoparticle concentration, ionic strength (IS), pH and bath sonication on the agglomeration behaviour of silica particles in solution has been systematically investigated. Moreover, the colloidal stability of silica particles in the presence of BSA has been investigated showing a correlation between silica and protein concentrations and the formation of agglomerates. Finally, the colloidal stability of silica particles in standard cell culture medium has been tested, concluding the necessity of surface modification in order to preserve silica as primary particles in the presence of serum. The results presented here have major implications on toxicity investigations because silica agglomeration will change the probability and uptake mechanisms and thereby may affect toxicity. © 2010 Springer Science+Business Media B.V.