Defects in motile cilia, cell surface organelles found in tissues such as the epithelial lining of the lungs, are linked to numerous diseases, including chronic respiratory disorders and disturbances in left-right (L/R) asymmetry,but what role does ciliary motility play in these diseases? On p. 1621, Serluca,Burdine and colleagues report that two mutations in the zebrafish seahorse gene, which encodes the leucine-rich repeat-containing protein Lrrc6l, disrupt ciliary motility and cause pronephric cysts, but rarely result in L/R patterning defects. The mutations do not affect pronephric patterning or overall cilia structure, but disrupt ciliary motility in the pronephros and the neural tube. However, their effect on fluid flow in Kupffer's vesicle (KV), a ciliated structure important for L/R asymmetry, is weaker and variable, and changes in KV fluid flow do not correlate well with L/R phenotypes. In addition, a previously reported seahorse mutation is known to cause pronephric cysts without disrupting ciliary motility. Thus,the authors suggest that the functions of seahorse in ciliary motility and in downstream cilia-related phenotypes are separate.