Some of the most challenging issues in biomineralization relate to understanding how organisms control the properties of the minerals and molecular crystals that they form. Here, we examine these largely unresolved issues by considering factors that could be involved in determining the specific crystal polymorph formed. We also focus on the interplay between control over the properties of transient disordered precursor phases and control exerted by crystal nucleation on pre-positioned structured surfaces. In most cases, the polymorph and/or mineral types used are clearly under genetic control, yet in only very few cases are we aware of an obvious functional benefit. This is exemplified by many molecular crystals in vision and production of structural colors, where polymorph type and function do not correlate. There are many common underlying control mechanisms common to the formation of carbonate and phosphate minerals, and molecular crystals. We conclude that in many cases control is being exerted both at the precursor phase stage, as well as at the nucleation stage, and suggest that this possible redundancy could be responsible for the high fidelity that organisms exhibit over crystal polymorph and molecular crystal types formed. Finally cholesterol crystal formation, provides good insights into polymorph choice and substrate control. We wonder whether this occurs because this is a pathological process that perhaps ‘obeys’ better the chemical laws that we understand, as opposed to the normal biological control exhibited through cells that appear to be far more complex.