In order to observe the individualization, migration and fate of neural crest cells, they must be examined in vivo. However, due to the immense number of cells in the embryo, neural crest cannot be tracked in situ under a microscope. Therefore, a number of natural markers on neural crest cells are used to trace their migrations to definitive target sites in the embryo. The enzyme acetylcholinesterase is expressed in early migrating crest cells, and is used to perform neural crest fate maps and migration pathways. The slug gene, which encodes a zinc finger transcription factor, is also strongly expressed in the neural crest precursor cells prior to migration. The presence of slug transcripts decreases during differentiation, when transcription of the gene stops. Growth factor receptors of the protein tyrosine kinase are also present in the neural fold and maintained in the neural crest cells as they begin to migrate. All these molecules can be tracked to identify the location of neural crest cells.

The chick-quail marker system is another method to track the migration and fate of neural crest cells. Quail cells contain a large nucleolus due to a mass of heterochromatin, and can be easily stained by the Feulgen-Rossenbeck reaction. In contrast, the chromatin in chick cells is evenly distributed in the nucleoplasm. Therefore, the nucleolus cannot be detectably stained by the Feulgen-Rossenbeck reaction. (Le Douarin, 10)

Researchers used this important distinction to view the progress of grafted quail cells in chick embryos (particularly in the neural crest region). After embryogenesis, the sectioned embryos were stained and viewed with light and electron microscopy to generate fate maps and determine neural crest derivatives.

Another, more advanced, technique is to use radioisotopically labeled cells in place of neural crest in an unlabeled host chick embryo. Weston and Johnston pioneered this technique in the 1960s.