In this review article, CE methods for analysis of biologically important thiols are overviewed. The article covers the period from the previously published comprehensive review in 2004 until mid-2016, with emphasis on various detection modes, novel approaches for sample preconcentration, and applications in clinical practice. The most commonly used detection methods, such as conductometry or absorbance detection, although universally applicable and available in most commercial instruments have low sensitivity and have only limited use in thiol analysis. Amperometric and MS detection are more sensitive and have their steady place in thiol analysis, although the mainstay remains CE with LIF detection, reaching nanomolar concentration sensitivities for most of the thiols. Novel probes for CE-LIF have been developed and tested. The preconcentration approaches using modified gold nanoparticles reaching excellent sensitivities in the picomolar range and various sample stacking methods are also reviewed. Finally, significant clinical applications of the developed methods are discussed with critical insights into the future of CE analysis of thiols.