Size exclusion chromatography (SEC) is a historical technique, routinely applied for the separation of species possessing different molecular masses (sizes). It is considered as a reference method for the qualitative and quantitative analysis of protein aggregates. In the last few years,several improvements were brought to high performance SEC (HP-SEC or conventional SEC) in terms of particle size, inertness and column dimension. Today, SEC columns of smaller dimensions packed with sub-3 μm particles (also known as ultra-high performance SEC (UHPSEC)) are used, to obtain faster and better separation compared to HP-SEC. This paper discusses the possibilities and limitations of both HP-SEC and UHP-SEC and also describes some possible directions for future applications related to protein biopharmaceuticals analysis.