This paper describes the development of medical applications for polyhydroxyalkanoates (PHAs), a class of natural polymers with a wide range of thermoplastic properties. Methods are described for preparing PHAs with high purity, modifying these materials to change their surface and degradation properties, and methods for fabricating them into different forms, including tissue engineering scaffolds. Preliminary reports characterizing their in vivo behavior are given, as well as methods for using the natural polymers in tissue engineering applications.