Step 1: Congenital tuberculosis is rare because a mother with active tuberculosis often presents with infertility. When transmission does occur, the route of spread determines the organ that is first affected.
Step 2: The tubercle bacilli most commonly pass from the mother through the umbilical vein to the fetus. The umbilical vein drains into the fetal liver, so a primary focus, the hepatic primary complex, develops there. This makes the liver the most commonly involved organ.
Step 3: If the neonate instead aspirates amniotic fluid containing bacilli, gastrointestinal or lung infection can follow, which is why lung is a tempting but less common answer. Neonates usually present with respiratory distress, hepatosplenomegaly and lymphadenopathy. The pancreas and kidney are not characteristic primary sites, so the correct answer is liver.