Annexin V belongs to the annexin family of calcium-dependent phospholipid binding proteins and has a high affinity for phosphatidylserine (PS). One of the characteristic features of early stage apoptosis is the translocation of PS from the inner to the outer leaflet of the plasma membrane, exposing it to the extracellular environment where it can be detected. Fluorochrome conjugated Annexin V can serve as a sensitive detection probe for this hallmark of early stage apoptotic change.

Annexin V is generally used in combination with a viability dye, such as 7-AAD or propidium iodide (PI), that cannot pass through intact cellular membranes. Translocation of PS occurs prior to loss of membrane integrity, therefore viability dyes would be excluded from the cell. As cells progress through the apoptotic process, membranes are compromised and the viability dyes are able to enter the cell. Using this method, cells that are Annexin V positive and viability dye negative are in early apoptosis. If cells are positive for both Annexin V and the viability dye, they are either undergoing apoptotic death or necrosis. When negative for both markers, cells are viable.