Based on the concept of magnetofection, we prepared lipid shell microbubbles loaded with highly positively charged iron oxide magnetic nanoparticles through electrostatic and matrix affinity interactions. These magnetic microbubbles showed strong ultrasound contrast. When the magnetic microbubbles were mixed with plasmid DNA encoding a reporter gene, gene delivery to HeLa cells was achieved only when ultrasound was applied. Gene transfer efficiency strongly depended on the application of a gradient magnetic field. Treatment of HeLa cells with the microbubbles and ultrasound resulted in strong concentration‐dependent cytotoxic effects, whereas ultrasound alone, lipid microbubbles alone, magnetic nanoparticles or magnetic microbubbles alone did not significantly affect cell viability. These magnetic microbubbles could be used as magnetically targeted diagnostic agents for real‐time ultrasound imaging or for cancer therapy, therapy of vascular thrombosis and gene therapy.