Alphafetoprotein (AFP) is an oncofetal glycoprotein that frequently reappears in sera of patients affected by hepatocellular carcinoma (HCC) and yolk-sac tumours (YST). In these cases AFP determination represents a useful marker for monitoring the therapeutic response and the clinical evolution of the neoplastic disease. AFP is a heterogeneous molecule with respect to the carbohydrate moiety and the different AFP glycoforms can be separated and characterized by their affinity for lectins, such as Concanavalin A (con A), and Lens culinaris agglutinin (LCA). Increased production of LCA-reactive AFP has been proposed as a specific and early marker for HCC, while Con A non-reactive AFP could be a marker for YST and gastrointestinal malignancies. In this review the molecular basis of AFP microheterogeneity and the clinical application of AFP isoforms will be discussed.