Forkhead box protein J1 (FOXJ1) is a transcription factor that can suppress T cell activity, through the repression of NF-κβ activity. Its dysregulation is associated with autoimmune diseases and inflammatory diseases. FOXJ1 plays a critical role in the maintenance of immune homeostasis. This involves intricate interactions between the forkhead family members and inflammatory transcription factors. It coordinates the regulation of the activity of two key inflammatory transcription factors, NF-AT and NF-κβ. It has also been shown that FOXJ1 has fundamental roles in ciliogenesis in the lung and is directly required for epithelial cell ciliogenesis of the neonatal oviduct.