Methylxanthines and methyluric acids are secondary metabolites derived from purine nucleotides and are known collectively as purine alkaloids. The present review begins by summarizing the distribution of these compounds in the plant kingdom, and then provides an up-to-date account of the biosynthesis of purine alkaloids. The diversity of biosynthesis and accumulation between species and between tissues of different age is considered. We also discuss the physiological function of these purine alkaloids in plants and the biotechnology for creating caffeine-free plants.