Polyhydroxyalkanoates (PHA) are natural, thermoplastic polyesters and due to their biocompatible and biodegradable properties they are good alternatives for the production of scaffolds for engineered tissues or nanoparticles for drug delivery. As a member of polyhydroxyalkanoate family, polyhydroxybutyrates (PHB) have been widely used as a biomaterial for in vitro and in vivo studies since their mechanical properties are very similar to conventional plastics. By using multi-emulsion technique, iron oxide particles were coated with polyhydroxybutyrate (PHB) polymer synthesized from Alcaligenes eutrophus bacteria and the magnetic carrier system was prepared accordingly. The bare nanoparticles and magnetic nanoparticles were morphologically, structurally and magnetically characterized by using Scanning electron microscope (SEM) and Atomic force microscope (AFM); Fourier Transform Infrared Spectrometry (FTIR), and Electron Spin Resonance (ESR) and Vibrating Sample Magnetometer (VSM) techniques, respectively. Particle size of PHB nanoparticles was determined by Zeta Sizer. It was found that the smallest particles were in the range of 239,43±5,25 nm in diameter. Concanavalin-A (Con-A) was used for targeting the cancer cells while etoposide was used as drug. Con-A and etoposide were loaded onto the particles. Release studies of etoposide were evaluated and the system was optimized for the further in vivo applications. Finally different formulation magnetic PHB nanoparticles cytotoxicity were evaluated in cell culture studies and used HeLa cell line (cervical cancer cells) as a cancer cells and L929 cells (mouse fibroblast cells) as a non-cancer cell line. Copyright © 2012 American Scientific Publishers All rights reserved.