Cilia are essential for normal organ function and developmental patterning, but their role in injury and regeneration responses is unknown. To probe the role of cilia in injury, we analyzed the function of foxj1, a transcriptional regulator of cilia genes, in response to tissue damage and renal cyst formation. Zebrafish
foxj1a
, but not
foxj1b
, was rapidly induced in response to epithelial distension and stretch, kidney cyst formation, acute kidney injury by gentamicin, and crush injury in spinal cord cells. Obstruction-induced up-regulation of
foxj1a
was not inhibited by cycloheximide, identifying
foxj1a
as a primary response gene to epithelial injury. Foxj1 was also dramatically up-regulated in murine cystic kidney disease epithelia [
jck/jck (nek8)
and
Ift88Tg737Rpw
−/−
] as well as in response to kidney ischemia-reperfusion injury. Obstruction of the zebrafish pronephric tubule caused a rapid increase in cilia beat rate that correlated tightly with expanded tubule diameter and epithelial stretch. Zebrafish
foxj1a
was specifically required for cilia motility. Enhanced
foxj1a
expression in obstructed tubules induced cilia motility target genes
efhc1
,
tektin-1
, and
dnahc9. foxj1a
-deficient embryos failed to up-regulate
efhc1
,
tektin-1
, and
dnahc9
and could not maintain enhanced cilia beat rates after obstruction, identifying an essential role for
foxj1
in modulating cilia function after injury. These studies reveal that activation of a Foxj1 transcriptional network of ciliogenic genes is an evolutionarily conserved response to multiple forms of tissue damage and highlight enhanced cilia function as a previously uncharacterized component of organ homeostasis.