The FoxA genes belong to a conserved family of transcription factors, that play a crucial role in regulating embryonic development, cellular differentiation, and disease pathogenesis. Initially identified as hepatocyte nuclear factor 3α (Hnf3α), FoxA is pivotal in activating liver-specific genes and contributing to liver morphogenesis. Studies have shown that FoxA proteins interact with specific DNA sequences and nucleosome-bound DNA, altering the local chromatin structure to regulate gene expression. The unique ability has earned them the designation of “pioneer factors”. The FoxA family comprises three members: FoxA1, FoxA2, and FoxA3. FoxA1 is predominantly expressed in endoderm-derived organs such as the lungs, liver, pancreas, and prostate, where it regulates hormone metabolism, cell cycle, and cell proliferation. FoxA2 is primarily expressed in the floor plate of the vertebrate spinal cord, where it plays a key role in establishing the dorsal-ventral patterning of the neural tube. FoxA3 is mainly expressed in the testes, where it regulates germ cell formation. FoxA genes exhibit functional diversity in embryonic development across different species, offering insights into their evolutionary roles. For instance, zebrafish embryos with mutations in the foxa2^-/- gene can survive, providing an opportunity to study embryonic development mechanisms. Currently, a growing body of research suggests that FoxA genes are involved in early embryonic development, cancer, and metabolism-related diseases. This paper summarizes the discovery, expression patterns, and biological functions of the FoxA genes while identifying key scientific questions that remain unresolved. It aims to provide readers a solid scientific basis for understanding the molecular mechanisms through which FoxA genes regulate embryonic development and contribute to cancer pathogenesis.