Adsorption of 3-aminopropyltriethoxysilane (APTS) on magnetite nanoparticles during its formation has been investigated to optimise the preparation of stable aqueous dispersion of amine derivatised magnetite nanoparticles. APTS adsorbs chemically on the surface of magnetite particle modifying its surface which is evident from thermal and C, H, N analysis. The variation of particle size has been observed with change of APTS concentration. X-ray diffractogram shows the formation of pure inverse spinel phase magnetite with average crystallite size 7 nm when equimolar (Fe3O4: APTS = 1:1) quantity of APTS was used during its synthesis. The presence of free surface-NH2 groups and Fe-O-Si bonds was observed by FTIR. Raman spectrum further confirms the presence of surface-NH2 groups. Transmission electron microscopy shows formation of particles of average size between 7 nm and 12 nm. The effective hydrodynamic diameter of the APTS coated particle agglomerates is 45.8 nm in stable aqueous colloidal dispersion, which is evident from photon correlation spectroscopy. VSM measurements at room temperature of both silanised and unsilanised magnetite shows their superparamagnetic nature with saturation magnetisation 41 e.m.u/g and 56 e.m.u/g, respectively. Avidin has been immobilised on the surface through glutaraldehyde, which demonstrates the possibility of the synthesised material to be used in protein immobilisation to form bioactive magnetic particles.