Three GGAs (GGA1-3) were found in humans, among which GGA3 has short and long forms of spliced variants (GGA3-S and GGA3-L). The present study analyzed expression patterns of both GGA3 variants in human tissues and cell lines. Western blot analysis revealed that the brain contained both GGA3-S and -L, while other tissues and cell lines examined predominantly expressed GGA3-S. By double immunofluorescence microscopy, GGA1 and GGA3 were localized with slightly different patterns in both the trans-Golgi network (TGN) and peripheral region. When the dominant-negative mutant, VHS-GAT domain, of GGA1 or GGA3-L was overexpressed, TGN-associated GGA1 was redistributed into the cytoplasm. However, the GGA3 distribution was not affected by the expression of either VHS-GAT domain. These results indicate that GGA3-S which would not be directly involved in the cargo protein recognition is predominantly expressed in human tissues except the brain and in cell lines.