PURPOSE: The deposition of magnetic particles was examined for the possibility of further enhancing the selectivity of inhalation drug administration for the treatment of lung cancer. METHODS: Superparamagnetic magnetite nanoparticles were prepared and ultrasonically atomized, dried, and passed through glass tubes in the presence and absence of a wedge-shaped permanent magnet. The change in the outlet aerosol size distribution due to magnetic deposition under various well-defined aerodynamic conditions and a measured magnetic field was determined by an aerodynamic particle sizer. In addition, computational fluid dynamics (CFD) simulations of magnetic aerosol transport and deposition were conducted. RESULTS: The deposition fraction increased nearly linearly with particle diameter and was greater with lower air flow rates. The effect of tube diameter was complicated but well described by CFD simulations, as was the effect of particle size and air flow rate. CONCLUSIONS: The descriptive power of CFD simulations was demonstrated in the in vitro deposition of magnetic aerosol particles. This suggests that CFD simulations can potentially be used in future studies to design systems for selective drug delivery in vivo as a function of magnetic properties, aerosol characteristics, and respiratory physiology.