The microtubule (MT) cytoskeleton plays crucial roles in brain development by regulating the proliferation of neuronal progenitor cells, neuronal migration and axon guidance. Methods for monitoring MT in the intact brain, however, have been limited in vertebrates. Here, we report a transgenic zebrafish line for monitoring MT in vivo. This reporter line carries a transgene encoding the green fluorescent protein (GFP) -tagged tubulin gene linked to the upstream activating sequence (UAS), the recognition sequence of the yeast Gal4 transcriptional activator. By crossing this reporter line with appropriate transgenic Gal4 driver lines, we induced the GFP-tagged tubulin in various cell types from the embryonic stages to the adult stage. In larvae expressing the modified tubulin, individual MT filaments and other MT structures, including the mitotic spindles in proliferating neuronal progenitor cells, were clearly visualized. Therefore, the transgenic UAS reporter line should be useful for directly monitoring MTs in the intact brain.