Separations of bare superparamagnetic magnetite nanoparticles (BSPMNPs, approx. 11 nm diameter) was performed using non-complexing (nitrate) and complexing (chloride, citrate and phosphate) electrolyte ions with additions of tetramethylammonium hydroxide (TMAOH), which is commonly applied to control the synthesis of stable iron oxides. The use of TMAOH as a background electrolyte (BGE) additive for capillary electrophoresis (CE) separations provided for the first time electropherograms of BSPMNPs exhibiting symmetrical and highly reproducible peaks, free of spurious spikes characteristic of nanoparticle clusters. Consequently, accurate determination of the electrophoretic effective mobility of BSPMNPs was possible, yielding a value of -3.345E-08 m(2) V-1 s(-1) (relative standard deviation (RSD) of 0.500%). The obtained mobilities of BSPMNPs in the presence of various electrolyte ions show that the degree of complexation with the surface of BSPMNPs follows the order chloride < citrate < phosphate, correlating with the stabilities of Fe(III) complexes with the respective anions. Finally, bare and carboxylated iron oxide nanoparticles were successfully separated in only 10 min using 10 mM Tris-nitrate containing 20mM of TMAOH as electrolyte. Our findings show that simple and rapid CE experiments are an excellent tool to characterise and monitor properties and interactions of iron oxide nanoparticles with other molecules for surface modification purposes.