Experiments that led to the development of chromatographic methods traceable to the early 19^th century works of C.S. Schonbein, F. Goppelsroeder, R.E. Liesegang, and A. Martin used paper as the stationary medium. Martin and his collaborators used filter paper strips as carriers for the analysis of amino acid mixtures. Soon the technique was being used for all classes of natural products. Despite the introduction of more successful methods such as TLC, PC remains the method of choice for the analysis of water soluble compounds such as carbohydrates, amino acids, nucleic acid bases, organic acids, and phenolic compounds.

The mixture whose components are to be resolved is placed as a spot near one end of a rectangular filter paper strip. It is made to dip into a solvent mixture contained in a closed chamber saturated with the solvent vapor, such that the spotted mixture stays above the level of the solvent in the chamber. As the solvent moves up the paper by capillary effect, the components move along at different rates based on their partition coefficient between the solvent and the aqueous hydration shell of the paper cellulose fiber. After completing the development, the paper is dried and the position of the separated components visualized by the use of suitable developing agents.

PC is a form of planar chromatography as the stationary phase is planar in nature. The filter paper is both the support and the stationary phase. The technique may be modified as descending chromatography; when the arrangement is such, the solvent moves down the paper. When it moves from the center toward the circumference of a circular paper strip, it is radial PC. Two-dimensional chromatography refers to the technique when the PC is developed in two different solvents successively, the second solvent run in a direction perpendicular to the first solvent.

Electrochromatography is a form of charge based separation in which a filter paper strip is impregnated with a buffer supported in the center. Either ends of the paper dip into solutions in which electrodes are immersed. A spot of mixture to be separated is placed on the paper and electrical voltage applied across the electrodes. According to their charge, solutes move toward oppositely charged electrodes. Amino acid mixtures may be effectively separated using this technique.

PC involves separation based on either partitioning or adsorption. When the solvent is water-immiscible or partially soluble in water such as butanol, phenol, amyl alcohol, the separation is based on partitioning between the solvent and the water of hydration of cellulose fiber of the paper. Amino acids, alkaloids, phenols, anthraquinone derivatives, steroids, volatile terpenes, and sugars are separated on paper by partitioning.

When the solvent is water, adsorption forces bring about separation. Glycosides, nucleic acids, organic acids, and phenolic compounds may be separated using water as solvent.

Two-dimensional chromatography is especially applicable for the separation of amino acids and flavonoids. Choice of solvent is dependent on the nature of the constituent and its relative polarity, and resolution of mixtures on the chosen solvent may be improved by altering its acidity using ammonia, acetic acid, hydrochloric acid, etc. Alternatively, filter papers may be modified to reduce polarity of cellulose by impregnating it with silicic acid or alumina, hence making them more amenable for separation of nonpolar compounds such as lipids. Good separations on PC are indicated by well-defined, compact spots. The quantity of substance present determines the size of the spot in a particular solvent and this is used as the basis of quantitative evaluation.

For preparative purposes, thicker sheets of paper are used. Compounds separated from the mixture after development on PC can be eluted individually from the chromatogram by treating the cut-out spots with appropriate solvent and estimated by measuring its absorbance or fluorescence in the visible or UV region. PC may be used effectively for the quantitation of several alkaloids, anthraquinones, and volatile oils in extracts of their source herbs.

One of the significant advantages of PC is the reproducibility of R_f values. R_M (Log1/ Rf-1) is a more constant parameter for analysis of a series of structurally related compounds, such as flavonoids, glycosides, so much so it is possible to relate it effectively to chemical features such as number of hydroxyl groups attached. This even aids estimation of R_f values of an unknown member of a compound series.

Phenyl propanoids, lignans, all classes of flavonoids except isoflavones and xanthones, hydrolysable tannins, topolones, carotenoids, organic acids, glucosinolates, non-protein amino acids, amines, alkaloids, and sugars can be analyzed by PC.