In the malignant subtype of human intrahepatic cholangiocarcinoma, the loss of ARID1A was an independent prognostic factor for the overall survival of patients (p = 0.023); ARID1A and histone deacetylase 1 (HDAC1) were directly recruited to the ALDH1A1 promoter region in cholangiocarcinoma cells with undetectable ALDH1A1 expression. Here, ALDH1A1 is linked to cholangiocarcinoma.