Functional nucleotide analysis is a broad spectrum of techniques used to analyze a genome's functional aspects, particularly the constituent nucleotides. Such functional nucleotide analysis could be used to identify mutation and polymorphism – for example, single nucleotide polymorphism analysis.

As functional nucleotide analysis involves handling genetic material, a high degree of care is required. Analytical techniques can include sequencing, microarrays, or genetic interaction mapping.

Functional nucleotide analysis is most commonly used for research purposes. It can identify alterations to the genetic code of viruses, bacteria, or humans, detecting genetic diseases or mutation rates.