Method and apparatus for dynamically connecting modules within a programmable device is described. In an example, a programmable device is programmed with modular circuits. A bitstream is obtained from a database. The bitstream includes a first portion associated with a module and a second portion associated with an interface to the module. The bitstream is then modified with configuration data to connect the interface to one or more of the modular circuits. The programmable device is then configured using the modified bitstream.