The recent development of high spatial resolution analytical methods for inorganic element imaging enables the sensitive determination of inorganic and organometallic-based pesticides, at the cellular and subcellular levels. Some organic agrochemicals can also be investigated providing they contain one or more hetero-element, such as the halogens fluorine or bromine. Several micro-chemical imaging methods are currently available and will be reviewed in this article: Electron Microscopy combined to Energy Dispersive X-ray Spectrometry (EM-EDS), PIXE (Particle Induced X-ray Emission), SXRF (Synchrotron Radiation X-ray Fluorescence) combined to micro-XAS (X-ray Absorption Spectroscopy), and Secondary Ion Mass Spectrometry (SIMS). Although these methods offer a high potential in the understanding of the cellular mechanisms of pesticides toxicity, they have not been much used yet in this domain of investigation. The aim of this article is to make known these imaging methods to the scientific community interested in the toxicology of pesticides. Some examples of applications taken from our own investigations, and from other researchers, will be presented to illustrate the kind of information can be gathered from these methods. In particular, the subcellular distribution of Maneb in neuronal cells will be discussed, as well as the subcellular chemical speciation of arsenic in human ovarian cells.