Vernix suspended in amniotic fluid is normally swallowed by the late term fetus. We hypothesized that branched chain fatty acids (BCFA), long known to be major vernix components, would be found in meconium and that the profiles would differ systematically. Vernix and meconium were collected from term newborns and analyzed. BCFA-containing lipids constituted about 12% of vernix dry weight, and were predominantly saturated, and had 11–26 carbons per BCFA. In contrast, meconium BCFA had 16–26 carbons, and were about 1% of dry weight. Meconium BCFA were mostly in the iso-configuration, whereas vernix BCFA contained dimethyl and middle chain branching, and five anteiso-BCFA. The mass of BCFA entering the fetal gut as swallowed vernix particles is estimated to be 180 mg in the last month of gestation whereas the total mass of BCFA found in meconium is estimated to be 16 mg, thus most BCFA disappear from the fetal gut. The BCFA profiles of vernix and meconium show that BCFA are major components of normal healthy term newborn gastrointestinal tract. BCFA are candidates for agents that play a role in gut colonization and should be considered a nutritional component for the fetus/newborn.