Recently, optically reconfigurable gate arrays (ORGAs) consisting of a gate array VLSI, a holographic memory, and a laser array have been developed to achieve a huge virtual gate count that is much larger than those of currently available VLSls. Consequently, ORGAs with more than tera-gate capacity will be realized by exploiting the storage capacity of a holographic memory. However, in contrast to current field-programmable gate arrays (FPGAs), conventional ORGAs have an important shortcoming: alignment errors arise when a programmable ORGA is recorded with a writer system. When programming a programmable ORGA along with alignment errors between the programmable ORGA and its writer system, the reconfiguration speed of the programmable ORGA is decreased. This paper therefore presents a detection and compensation method of alignment errors between a programmable ORGA and a writer system to alleviate that shortcoming.