Anti-Golgi autoantibodies (AGAs) and their targets have been reported from several diseases. However, the association of AGAs, selective autoantigens and related clinical diseases is still obscure. In this study, the presence of AGAs in the sera of 5983 patients was screened to explore the association of AGAs and clinical diseases. By means of indirect immunofluorescence using HEp-2 cells, sera of 12 patients bearing AGAs were identified. The location of recognized Golgi autoantigen(s) was confirmed by the treatment of monensin and double immunostaining using beta-COP. Using the immunoelectron microscopy, AGA immunoreactivity was clearly demonstrated at a stack structure, characteristic of the Golgi complex. Furthermore, analysis of the 12 AGA-positive sera by Western blot revealed at least 15 components of Golgi antigens with relative molecular weights ranging from 54 to 350 kDa, and several Golgi autoantigens identified may be novel. Notably, over half of the AGA-positive cases found belong to non-autoimmune diseases, particularly hepatic disorder. This study presents the association of AGAs, components of the Golgi complex and clinical diseases.