During mitosis, the mammalian Golgi disassembles into numerous vesicles and larger membrane structures referred to as clusters or remnants. Following mitosis, the vesicles and clusters reassemble to form an intact Golgi in each daughter cell. One model of Golgi biogenesis states that Golgi matrix proteins remain assembled in mitotic clusters and then serve as a template for Golgi reassembly. To test this idea, we performed a 3D-computational analysis of mitotic cells to determine the extent to which these proteins remain in mitotic clusters. As a control we used brefeldin A-induced Golgi disassembly which causes dispersal of Golgi enzymes, but leaves matrix proteins in remnant structures. Unlike brefeldin A-treated cells, in which matrix proteins were clearly sorted from non-matrix proteins, we observed extensive dispersal of matrix proteins in metaphase cells with no evidence of differential sorting of these proteins from other Golgi proteins. The extensive disassembly of matrix proteins argues against their participation in a stable template and supports a self-assembly mode of Golgi biogenesis.