A first database implemented on a remote device such as a handheld computer may be reconciled with a corresponding second database implemented on a host computer during execution of an application program on the handheld device. In addition, the application program may be executed according to program instructions stored in an application program file located in the remote device. The databases may be reconciled by first commencing execution of the application program. Then, during the course of program execution, a synchronization instruction located in said application program file is retrieved. The synchronization instruction is executed by establishing a communications link between the handheld computer and the host computer. Subsequently, any differences between the first database and the second database are reconciled. Furthermore, embodiments of the invention contemplate that in addition to reconciling all of the databases located on the handheld and host computers, less than all of the databases may be reconciled to reduce the amount of time required to execute the reconciliation process. In addition, after reconciliation control may be returned to the calling application program, or to another application, as determined by the application designer.