In the present work, three zebrafish cDNA clones encoding transferrin, intestinal fatty acid binding protein (IFABP), and elastaseB were cloned and their expression patterns in early zebrafish development were characterized as differentiation markers for the three major endoderm organs: liver, intestine, and exocrine pancreas. transferrin and ifabp mRNAs exhibit a biphasic expression pattern during early development. transferrin mRNAs were first expressed at ∼7 hours postfertilization (hpf) in the yolk syncytial layer (YSL) and later in the liver rudiment (from ∼48 hpf) and in the esophagus transiently (72–96 hpf). Ifabp mRNAs were initially expressed in the YSL at the ventral side during late epiboly (8–9 hpf), spread throughout the YSL of later stage embryos, and appeared in the intestine rudiment at ∼36 hpf. In contrast to the transferrin and ifabp mRNAs, elastaseB mRNAs were not expressed in the yolk sac or YSL, and these transcripts were detected exclusively in the exocrine pancreas after ∼56 hpf. Developmental Dynamics 230:165–173, 2004. © 2004 Wiley‐Liss, Inc.