Size-exclusion chromatography, also known as molecular sieve chromatography, is a chromatographic method in which molecules in solution are separated by their shape, and in some cases size. It is usually applied to large molecules or macromolecular complexes such as proteins and industrial polymers. Typically, when an aqueous solution is used to transport the sample through the column, the technique is known as gel filtration chromatography, versus the name gel permeation chromatography, which is used when an organic solvent is used as a mobile phase. The chromatography column is packed with fine, porous beads which are commonly composed of dextran, agarose, or polyacrylamide polymers. The pore sizes of these beads are used to estimate the dimensions of macromolecules. SEC is a widely used polymer characterization method because of its ability to provide good molar mass distribution (Mw) results for polymers.

Size-exclusion chromatography (SEC) is fundamentally different from all other chromatographic techniques in that separation is based on a simple procedure of classifying molecule sizes rather than any type of interaction.

The main application of size-exclusion chromatography is the fractionation of proteins and other water-soluble polymers, while gel permeation chromatography is used to analyze the molecular weight distribution of organic-soluble polymers. Either technique should not be confused with gel electrophoresis, where an electric field is used to "pull" molecules through the gel depending on their electrical charges. The amount of time a solute remains within a pore is dependent on the size of the pore. Larger solutes will have access to a smaller volume and vice versa. Therefore, a smaller solute will remain within the pore for a longer period of time compared to a larger solute.

Even though size exclusion chromatography is widely utilized to study natural organic material, there are limitations. One of these limitations include that there is no standard molecular weight marker; thus, there is nothing to compare the results back to. If precise molecular weight is required, other methods should be used.

The advantages of this method include good separation of large molecules from the small molecules with a minimal volume of eluate, and that various solutions can be applied without interfering with the filtration process, all while preserving the biological activity of the particles to separate. The technique is generally combined with others that further separate molecules by other characteristics, such as acidity, basicity, charge, and affinity for certain compounds. With size exclusion chromatography, there are short and well-defined separation times and narrow bands, which lead to good sensitivity. There is also no sample loss because solutes do not interact with the stationary phase.

The other advantage to this experimental method is that in certain cases, it is feasible to determine the approximate molecular weight of a compound. The shape and size of the compound (eluent) determine how the compound interacts with the gel (stationary phase). To determine approximate molecular weight, the elution volumes of compounds with their corresponding molecular weights are obtained and then a plot of "K_av" vs "log(Mw)" is made, where ${\displaystyle K_{av}=(V_{e}-V_{o})/(V_{t}-V_{o})}$ and Mw is the molecular mass. This plot acts as a calibration curve, which is used to approximate the desired compound's molecular weight. The V_e component represents the volume at which the intermediate molecules elute such as molecules that have partial access to the beads of the column. In addition, V_t is the sum of the total volume between the beads and the volume within the beads. The V_o component represents the volume at which the larger molecules elute, which elute in the beginning. Disadvantages are, for example, that only a limited number of bands can be accommodated because the time scale of the chromatogram is short, and, in general, there must be a 10% difference in molecular mass to have a good resolution.

The technique was invented in 1955 by Grant Henry Lathe and Colin R Ruthven, working at Queen Charlotte's Hospital, London. They later received the John Scott Award for this invention. While Lathe and Ruthven used starch gels as the matrix, Jerker Porath and Per Flodin later introduced dextran gels; other gels with size fractionation properties include agarose and polyacrylamide. A short review of these developments has appeared.

There were also attempts to fractionate synthetic high polymers; however, it was not until 1964, when J. C. Moore of the Dow Chemical Company published his work on the preparation of gel permeation chromatography (GPC) columns based on cross-linked polystyrene with controlled pore size, that a rapid increase of research activity in this field began. It was recognized almost immediately that with proper calibration, GPC was capable to provide molar mass and molar mass distribution information for synthetic polymers. Because the latter information was difficult to obtain by other methods, GPC came rapidly into extensive use.