The analytical methodology for speciation of metals and metalloids associated with alkyl groups and biomacromolecules is critically reviewed. Alkylated metals and metalloids are not only known to be produced by microbial methylation within most anaerobic compartments in the environment, but also in the course of enzymatic transformations during human metabolism. Because of the toxicological relevance of these compounds present in trace to ultratrace concentrations, firm species identification and exact quantification are essential. While many instrumental techniques coupling chromatography (GC, HPLC, CE, GE) with plasma mass spectrometry (ICP-MS) are available for quantification, methods used for structural identification often suffer from inadequate sensitivity (EI-MS, ESI-MS, MALDI-MS, FT-ICRMS). Other problems encountered are sample derivatisation artefacts, lack of suitable standards for quantification, lack of equilibrium between spikes and sample, and the integrity of metal-protein association during separation, in particular during SDS-PAGE. Selected application examples with respect to mercury and arsenic speciation will be discussed critically.