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The chromosome segregation 1-like(Cse1l/CAS),a microtubule-associated protein,is distributed in human cells containing many microtubules,such as cilia and basal bodies of the columnar epithelium cells.In this study,we have found that knockdown of cse1l in zebrafish leads to phenotypes similar to zebrafish mutants with cilia defects,including hydrocephaly,cardiac edema,curved body,kidney cyst and abnormal number of otolith.In addition,zebrafish cse1l morphants demonstrate randomized heart looping and misexpression of early left-right asymmetric makers lefty1,lefty2 and southpaw.Proper ciliogenesis in Kupffer’s vesicle(KV)is very important for left-right patterning in zebrafish.Cilia dysfunction in pronephric ducts also results in cystic kidney disease.Analysis of cilia in KV and pronephros shows that both the length and number of cilia are reduced in cse1l-deficient embryos.These data indicate that cse1l is crucial for early embryonic development through the regulation of ciliogenesis in zebrafish.