The in vivo substitution of magnesium, the central atom of chlorophyll, by heavy metals (mercury, copper, cadmium, nickel, zinc, lead) leads to a breakdown in photosynthesis and is an important damage mechanism in heavy metal-stressed plants. In this study, a number of methods are presented for the efficient In situ detection of this substitution (i.e. in whole plants or in chloroplasts). While macroscopic observations point to the formation of heavy metal chlorophylls at higher concentrations, fluorescence microscopy enables the detection of this reaction at very low substitution rates. Therefore, the course of the reaction can be followed by continuously measuring the fluorescence of whole plants. Furthermore absorbance spectroscopy of whole cells or isolated chloroplasts also enables the In situ detection of heavy metal chlorophylls. These methods provide practicable approaches in detecting the formation of these compounds In situ, avoiding artefacts that might occur using extraction methods based on polar solvents. In addition to the new methods for In situ detection, an extreme heterogeneity in the reaction of cells in the same tissue upon heavy metal stress was observed: while some cells are already disintegrating, others still show normal fluorescence and photosynthetic activity. Measurements of fluorescence kinetics gave a further hint that in high light intensity a substitution of Mg by heavy metals might take place specifically in PS II reaction centres.