Polyoxometalates (POMs) are inorganic cluster compounds that have been shown to possess a number of pharmacological properties, including antidiabetic, antibacterial, antiprotozoal, antiviral and anticancer activities. Their molecular mechanism of action is largely unknown. However, several studies indicate that many of their activities may be due to the inhibition of enzymes, in particular, of those enzymes that are accessible from the extracellular space and do not require the penetration of cell membranes. In this review, we describe the recent progress in the preparation and optimization of POMs, and an evaluation of their use as inhibitors of different families of enzymes. The next important steps in this area of research will be to gain a better understanding of the interactions of POMs with enzymes on a structural level through an X-ray crystallographic study of enzyme–POM complexes and the analysis of structure–activity relationships. Furthermore, POMs with increased stability and in vivo half-lives have to be prepared. Surface modification may allow the targeting of POM drugs at their sites of action.