BACKGROUND: Kidney collecting ducts are comprised of principal cells and intercalated cells, with intercalated cells playing a crucial role in kidney acid-base regulation through H and HCO3 secretion. Despite its significance, the molecular mechanisms controlling intercalated cell development remain incompletely understood. METHODS: To investigate the specific role of Foxp1 in kidney tubular system, we specifically deleted Foxp1 expression in kidney distal nephrons and collecting ducts. We examined the effects of Foxp1 on intercalated cell differentiation and urine acidification. RNA sequencing and Chip-seq were used to identify Foxp1 target genes. To dissect the genetic network that regulates intercalated cell differentiation, Dmrt2-deficient mice were generated to determine the role of Dmrt2 in intercalated cell differentiation. Foxp1 deficient mice were cross with Notch2 deficient mice to dissect the relation between Foxp1 and Notch signaling. RESULTS: Foxp1 is selectively expressed in intercalated cells in collecting ducts. Absence of Foxp1 in kidney tubules led to the abolishment of intercalated cell differentiation in the collecting ducts, resulting in distal renal tubular acidosis. Foxp1 regulates the expression of Dmrt2 and Hmx2, two genes encoding transcription factors specifically expressed in type A and B intercalated cell cells, respectively. Further genetic analysis revealed that Dmrt2 is essential for type A intercalated cell differentiation, and Foxp1 is necessary downstream of Notch for the regulation of intercalated cell differentiation. CONCLUSIONS: Foxp1 is required for the renal intercalated cell differentiation and participated in acid-base regulation. Foxp1 regulated downstream transcriptional factors, Dmrt2 and Hmx2, which involved in the specification of distinct subsets of intercalated cells.