In portal hypertension, there is reduced portal blood flow to the liver, and as a result direct shunts between the portal and systemic blood systems open up, bypassing the liver. Fetor hepaticus is believed to be from a particular class of biological compounds called mercaptans that skip the liver via these porto-systemic shunts. Normally the liver would chemically modify them into odourless compounds, but since it now doesn't get the chance to do this, the mercaptans reach the lungs (and urine) largely unadulterated. And when they are breathed (or urinated) out, they give off their distinctive odour.
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