Anther culture has long been used for the production of fully homozygous lines in order to produce, mainly, doubled haploid plants, which are of great interest in plant breeding. For tomato, a recalcitrant species for androgenesis production protocols have not been standardized. It is known that the genotype, anther size, the developmental stage of the microspore, and the medium composition are some factors that can influence the calli production. The present study aimed to adapt flow cytometry methodology to verify the microsporogenesis phases of anthers in order to assess the anther responsiveness of different tomato genotypes in an androgenesis-induction culture medium and to analyze the DNA ploidy level of calli produced by flow cytometry. Anthers from flower buds of length 1.0 to 5.9 mm, corresponding to the size range as analyzed by flow cytometry and cytogenetic methods, were inoculated into Murashige and Skoog (MS) basal medium containing the growth regulators 6-(y,ydimethylallylamino) purine and indole-3-acetic acid. The obtained calli were subsequently analyzed by flow cytometry to determine the DNA ploidy level. Surprisingly, despite no pretreatment with microtubule-depolymerizing agents, five classes of multiploid calli were observed, as follows: class I (2C-4C-8C-16C), class II (2C-4C-8C-16C-32C), class III (4C-8C), class IV (4C-8C-16C) and class V (8C-16C-32C). Multiploid calli were identified in short-term (two month) culturing, suggesting that the variable culture duration did not directly influence the occurrence of endoreduplication. In this work, this type of somaclonal variation has been reported for the first time in tomato anther culture, and their possible origin has been discussed.