Emerging contaminants are a broad category of chemicals, previously unknown or unrecognized as being of concern, but which, because of their potential health effects associated with human exposure, are under increasing scrutiny. To accurately measure their levels in biological matrices, specific and sensitive analytical methods have recently been developed. We have reviewed here the methods used for analysis of selected emerging organic contaminants, for example metabolites of organophosphate triesters, metabolites of new phthalates or phthalate substitutes, perchlorate, organic UV filters, and polycyclic siloxanes, in human matrices. Although the use of new techniques and approaches has been emphasized, we also acknowledge methods previously used for other contaminants and adapted for the emerging contaminants listed above. In all cases, chromatography and mass spectrometry were the techniques of choice, because of their selectivity and sensitivity for measurements at ng g(-1) levels. Critical issues and challenges have been discussed, together with recommendations for further improvement in particular cases (e.g. metabolites of phthalates or their substitutes). In particular, the use of labeled internal standards, the availability of certified reference materials, and the need for interlaboratory comparison exercises are key aspects of further development of this field of research.