Provided are a method, system, and article of manufacture for checkpointing and restoring user space data structures used by an application accessing a data structure maintained by an operating system for an executing application. Information in the accessed data structure is saved with checkpoint information for the application. An operation to restore the application from the checkpoint information is initialized. A restored data structure is generated to include the saved information in the accessed data structure saved in the checkpoint information in response to restoring the application. An initialization routine of the application is modified to bypass initializing the data structure as part of the application initialization routine to restore the application.