Chlorophylls (Chls) are contained in all photosynthetic organisms ranging from higher plants to algae and some bacteria, and constitute a group of the most abundant metal complexes in nature. Higher plants possess two major Chl derivatives, Chl a and Chl b, whose separation by Tswett at the beginning of this century was the cradle of chromatography. Once extracted from living tissues, Chls are extremely susceptible to molecular alterations including pheophytinization (Mg release), epimerization, ester hydrolysis, and allomerization. This feature often raises serious problems in practical fields such as quality control of processed vegetables, human photo-hypersensitivity, and biosphere activity evaluation. In view of this, a number of methods have been proposed over the past decades for reliable determination of Chl derivatives. This article reviews recent developments and improvements with regard to extraction, separation, and quantitation of these natural pigments. In addition, a brief discussion is given on the requirement for analytical means with enough sensitivity and resolution in the molecular-level elucidation of photosynthetic mechanisms.