Understanding three-dimensional (3D) hepatobiliary architecture is fundamental to elucidating structure/function relationships relevant to hepatobiliary metabolism, transport, and toxicity. To date, factual information on vertebrate liver architecture in 3 dimensions has remained limited. Applying noninvasive in vivo imaging to a living small fish animal model we elucidated, and present here, the 3D architecture of this lower vertebrate liver. Our investigations show that hepatobiliary architecture in medaka is based on a polyhedral (hexagonal) structural motif, that the intrahepatic biliary system is an interconnected network of canaliculi and bile-preductules, and that parenchymal architecture in this lower vertebrate is more related to that of the mammalian liver than previously believed. The in vivo findings presented advance our comparative 3D understanding of vertebrate liver structure/function, help clarify previous discrepancies among vertebrate liver conceptual models, and pose interesting questions regarding the ''functional unit'' of the vertebrate liver. Anat Rec, 290:770-782, 2007. 2007 Wiley-Liss, Inc.