The use of mass spectrometry based on atmospheric pressure ionisation techniques (atmospheric pressure chemical ionisation, APCI, and electrospray ionisation, ESI) for speciation analysis is reviewed with emphasis on the literature published in and after 1999. This report accounts for the increasing interest that atmospheric pressure ionisation techniques, and in particular ESI, have found in the past years for qualitative and quantitative speciation analysis. In contrast to element-selective detectors, organic mass spectrometric techniques provide information on the intact metal species which can be used for the identification of unknown species (particularly with MS-MS detection) or the confirmation of the actual presence of species in a given sample. Due to the complexity of real samples, it is inevitable in all but the simplest cases to couple atmospheric pressure MS detection to a separation technique. Separation in the liquid phase (capillary electrophoresis or liquid chromatography in reversed phase, ion chromatographic or size-exclusion mode) is particularly suitable since the available techniques cover a very wide range of analyte polarities and molecular mass. Moreover, derivatisation can normally be avoided in liquid-phase separation. Particularly in complex environmental or biological samples, separation in one dimension is not sufficient for obtaining adequate resolution for all relevant species. In this case, multi-dimensional separation, based on orthogonal separation techniques, has proven successful. ESI-MS is also often used in parallel with inductively coupled plasma MS detection. This review is structured in two parts. In the first, the fundamentals of atmospheric pressure ionisation techniques are briefly reviewed. The second part of the review discusses recent applications including redox species, use of ESI-MS for structural elucidation of metal complexes, characterisation and quantification of small organometallic species with relevance to environment, health and food. Particular attention is given to the characterisation of biomolecules and metalloproteins (metallothioneins and phytochelatins) and to the investigation of the interaction of metals and biomolecules. Particularly in the latter field, ESI-MS is the ideal technique due to the softness of the ionisation process which allows to assume that the detected gas-phase ions are a true representation of the ions or ion-biomolecule complexes prevalent in solution. It is particularly this field, important to biochemistry, physiology and medical chemistry, where we can expect significant developments also in the future.