Mercury (Hg), arsenic (As) and selenium (Se) are ubiquitous in the environment and exist in a variety of species, which have great influence on their transport, bioaccumulation and toxicity. This review presents the recent research progress in speciation analysis of Hg, As, and Se, with emphasis on enhanced cold vapor generation as interface for liquid chromatography and atomic spectrometry, speciation of volatile species in gas phase, and isotope dilution technique to improve the precision and accuracy of speciation. Hyphenated techniques to characterize the complexes of Hg and As with phytochelatins and chromatographic separation coupled with multi-collector-inductively coupled plasma mass spectrometry to measure species-specific isotopic ratios, are also briefly discussed. Mercury (Hg) and arsenic (As) are among the most highly toxic elements for humans and ecosystems and can cause serious environmental and human health problems even at low concentrations [1,2]. Selenium (Se) is an "essential toxin" for human health. It has been recognized as an important antioxidant and anti-cancer element. However, Se can also pose negative impact such as defective skin and hair loss [3]. The adsorption/uptake, transport, bioaccumulation, metabolism and toxicity of these elements strongly depend on their chemical species present in environmental and biological samples. In the environment, one species can transform to another through chemical or biological processes. For example, in anaerobic sediments, sulfur-reducing or iron-reducing bacteria can methylate inorganic mercury into highly toxic methylmercury (MeHg) [4,5]. Therefore, speciation analysis of Hg, As and Se is of great importance in order to elucidate the biogeochemcal cycle and toxicology of these elements. Speciation analysis mainly involves chromatographic separation (gas chromatography (GC) or high performance liquid chromatography (HPLC)) hyphenated with element-specific spectrometry or molecular mass spectrometry. This review presents the recent advances in speciation analysis of Hg, As, and Se based on chromatographic separation, with emphasis on enhanced cold vapor generation (CVG) as interface for LC and atomic spectrometry, speciation of volatile Hg, As and Se in gas phase, and isotope dilution technique to improve the precision and accuracy of speciation. Hyphenated techniques to characterize the complexes of Hg and As with phytochelatins and chromatographic separation coupled with multi-collector-inductively coupled plasma mass spectrometry (MC-ICP-MS) to measure species-specific isotopic ratios, are also briefly introduced.