Biliary Atresia (BA) and Alagille Syndrome (ALGS) are cholestatic liver diseases that afflict children and often require liver transplants. In this study, we use liver biopsy samples from patients to identify 3 subpopulations of macrophages which we name: lipid-associated macrophages (LAM), monocyte-like macrophages (MLM), and adaptive macrophages (AM). These are distinct from the 2 main macrophage populations found in the healthy livers of children and adults which are likely distinguished by their origin and lifespan: long-lived tissue-resident Kupffer Cells (here called NM or Ped1) and newly arrived monocyte-derived macrophages (here called IM or Ped2).