Endopolyploidy occurs in many plant species and supports the process of differentiation of cells and organs. The functional role of endopolyploidy in plant cells remains poorly understood, mainly because the analysis is hampered by the fact that complex polyploid tissues usually include cells with different ploidy levels. During the development of tomato fruit, cells from the (fleshy) pericarp tissue become highly polyploid reaching DNA content barely encountered in other plant species (between 2C and 512C). To investigate the spatial and temporal distribution of endopolyploidy, it is necessary to address the DNA content of individual nuclei in situ. Populations of nuclei with different ploidy levels were isolated to characterize at the cytological level the consequences of endopolyploidy on the ultrastructure of nuclear and nucleolar chromatin, the nuclear shape and the relationship with other cellular organelles such as mitochondria. We were able to develop a new method based on BAC-FISH to determine in situ the ploidy level of different nuclei and consequently establish a ploidy map of tomato fruit pericarp. Based on this map, we demonstrated a link between the ploidy level, the complexity of nuclear shape and the number of mitochondria in the vicinity of polyploid nuclei. We were able to provide the first direct evidence that endoreduplication plays a role in the increased transcription of rRNA and mRNA in plant cells. We thus provided quantitative data in favour of the ‘karyoplasmic ratio’ theory and showed that endoreduplication is associated with a complex cellular re-organization during development of tomato fruit