Magnetic cobalt spinel ferrite nanoparticles coated with biocompatible polygalacturonic acid were functionalized with ligands specific for targeting expressed EphA2 receptors on ovarian cancer cells. By using such magnetic nanoparticle-peptide conjugates, targeting and extraction of malignant cells were achieved with a magnetic field. Targeting ovarian cancer cells with receptor specific peptide-modified magnetic nanoparticles resulted in cell capture from a flow stream in vitro and from the peritoneal cavity of mice in vivo. Successful removal of metastatic cancer cells from the abdominal cavity and circulation using magnetic nanoparticle conjugates indicate the feasibility of a dialysis-like treatment and may improve long-term survival rates of ovarian cancer patients. This approach can be applied for fighting other cancers, such as leukemia, once the receptors on malignant cells are identified and the efficacy of targeting ligands is established.