Magnetic nanoparticles represent an advanced tool in biomedicine because they can be simultaneously functionalized and guided using a magnetic field. Iron oxide magnetic nanoparticles precoated with oleic acid and bearing novel antimicrobial N-heterocyclic choline analogues, namely O-, N- and O,N-bis-undecyl-substituted N-(2-hydroxyethyl)-1,2,3,4-tetrahydroisoquinolinium derivatives, have been obtained as potential biomedical agents for drug delivery and antimicrobial therapy. Structural and size determinations for the novel synthesized magnetic nanosystems were carried out based upon magnetogranulometry, dynamic light-scattering measurements and X-ray diffraction analysis. The most expected iron oxide core diameter was 6.2-10.5 nm. The magnetization analyses showed that the particles are superparamagnetic at room temperature. Aqueous magnetic fluids of the synthesized nanoparticles were examined in vitro concerning Gram-positive (Staphylococcus aureus MSCL 334, Bacillus cereus MSCL 330) and Gram-negative (Escherichia coli MSCL 332, Pseudomonas aeruginosa MSCL 331, Proteus mirabilis MSCL 590) bacterial strains and fungi (Candida albicans MSCL 378, Aspergillus niger MSCL 324). It was found that the samples have magnetic properties and possess antimicrobial activity. The minimum inhibitory concentration against S. aureus for the most active magnetic fluid was determined as 16 μg ml<sup>-1</sup>.