Digoxigenin is considered a hapten, a small molecule with high immunigenicity used in many molecular biology applications. Other popular haptens include DNP (dinitrophenol), biotin, and fluorescein. In general, antibodies generated against haptens have higher affinities for their targets than other antibodies, so haptens are conjugated to other biological molecules as all-purpose immuno-tags. This is because anti-hapten antibodies have high affinities and are readily available, while antibodies may not be commercially available for exotic biological targets.

Digoxigenin is a standard immunohistochemical marker for in situ hybridization. In this case it is conjugated to a single species of RNA nucleotide triphosphate (typically uridine), which is then incorporated into RNA (a "riboprobe") as it is synthesized by the cellular machinery. Later, the digoxigenin ("Dig") markers are detected with anti-digoxigenin antibodies, which may be labeled with dyes or enzymes (see ELISA) for visualization and detection. In a similar manner, digoxigenin may be conjugated to sugars to study glycosylation events in biological systems.

Digoxigenin is a standard immunohistochemical marker for in situ hybridization. In this case it is conjugated to a single species of RNA nucleotide triphosphate (typically uridine), which is then incorporated into RNA (a "riboprobe") as it is synthesized by the cellular machinery. Later, the digoxigenin ("Dig") markers are detected with anti-digoxigenin antibodies, which may be labeled with dyes or enzymes (see ELISA) for visualization and detection. In a similar manner, digoxigenin may be conjugated to sugars to study glycosylation events in biological systems.