Chlamydomonas reinhardtii controls flagellar assembly such that flagella are of an equal and predetermined length. Previous studies demonstrated that lithium, an inhibitor of glycogen synthase kinase 3 (GSK3), induced flagellar elongation, suggesting that a lithium-sensitive signal transduction pathway regulated flagellar length (S. Nakamura, H. Takino, and M. K. Kojima, Cell Struct. Funct. 12: [369][370][371][372][373][374] 1987). Here, we demonstrate that lithium treatment depletes the pool of flagellar proteins from the cell body and that the heterotrimeric kinesin Fla10p accumulates in flagella. We identify GSK3 in Chlamydomonas and demonstrate that its kinase activity is inhibited by lithium in vitro. The tyrosine-phosphorylated, active form of GSK3 was enriched in flagella and GSK3 associated with the axoneme in a phosphorylation-dependent manner. The level of active GSK3 correlated with flagellar length; early during flagellar regeneration, active GSK3 increased over basal levels. This increase in active GSK3 was rapidly lost within 30 min of regeneration as the level of active GSK3 decreased relative to the predeflagellation level. Taken together, these results suggest a possible role for GSK3 in regulating the assembly and length of flagella.How cells regulate the size of their organelles is poorly understood. Cilia and flagella are of particular interest, as the precise regulation of their length is critical to their function. The importance of the correct assembly of these organelles, including maintenance of the appropriate length, is illustrated by studies involving intraflagellar transport (IFT). IFT is required for the assembly and maintenance of cilia and flagella in organisms ranging from Chlamydomonas reinhardtii (where it was first identified) to sea urchins, Tetrahymena thermophila, Caenorhabditis elegans, and mice (10). In the absence of IFT, cilia and flagella fail to form correctly, resulting in various human diseases, including polycystic kidney disease and retinal degeneration, and anomalous determination of the left-right axis during development (51). Ultrastructural studies of children suffering from a particular form of primary ciliary dyskinesia revealed the presence of abnormally long cilia within their respiratory tracts, resulting in recurrent respiratory infections (1, 39). This observation suggests that not only do cilia and flagella need to assemble properly but that they also need to be of appropriate and defined lengths.The green alga Chlamydomonas reinhardtii makes an ideal model organism for studies involving ciliary and flagellar assembly and length control. Chlamydomonas has two apically localized flagella that are maintained at equal lengths. Moreover, within a population of wild-type cells, flagellar lengths fall within a very narrow range. The maintenance of flagella of equal lengths as an active process was first demonstrated in the "long-zero" experiments of Rosenbaum et al. (52). In these experiments, cells were deflagellated under conditions that amputated only one...