Copolymers of poly(3-hydroxyoctanoate) (PHO) with carboxylic groups in lateral chains have been prepared by chemical modification of unsaturated bacterial polyesters. The oxidation of the pendant alkenes is complete and important loss in molecular weight of polymer was observed. The presence of repeating units containing pendant carboxy groups in the proportion of 25% has enhanced hydrophilicity of these new polymeric structures. Nanoparticles have been prepared from PHO and two functionalized derivatives, characterized by electronic microscopy and compared in view of bioactive molecules transport and release.