Metallothioneins (MTs) are a group of low molecular mass, cysteine-rich proteins with a variety of functions including involvement in metal homeostasis, free radical scavenging, protection against heavy metal damage, and metabolic regulation via Zn donation. The overexpression of MTs in proliferating cells is turning the attention to the study of MTs as novel promising marker of tumor diseases. Besides, levels of MTs in invertebrates and aquatic vertebrates well correlate with heavy metal pollution of an environment and, thus, serve as bio-environmental marker. It is not surprising that these proteins are of great interest not only for biochemists, molecular biologists clinical chemists, but also for environmental chemists and ecologists. Detection and quantification of MTs, which is needed in all above mentioned areas, is challenging due to the high cysteine content and relatively low molecular mass. This review is giving an overview of the analytical methods used for determination of MTs comprising a broad range of immunochemical, electrochemical as well as spectrometric methods, which have been optimized and even hyphenated with different separation methods to detect MTs. More attention is paid to the structural analysis of these proteins as well as the employment of analytical instruments for environmental, biochemical and clinical purposes.