Flow cytometry is used extensively for whole cell biology. However, subcellular components of cells, such as chromosomes, chloroplasts and mitochondria are still a challenge for each cytometrist. The small size of these particles in combination with the low number of target molecules squeeze flow cytometers to their limits. Certain techniques are already well established such as single chromosome analysis, others are still on the brink to be available for the general scientific community, e. g. the analysis of single mitochondria.