Flow cytometry was used to analyze the DNA content of nuclei isolated from four different shoot cultures growing in vitro, and from callus of Rubus chamaemorus. The protocol for isolation of the nuclei of this species was optimized. Flow cytometry proved to be a fast and accurate method for estimation of the genome size of R. chamaemorus, a species containing phenolic compounds in the cytosol, which affect fluorochrome accessibility to DNA. Analyses showed that there is no variation in the ploidy level among different types of tissue cultures: axillary shoots from the 3rd and 20th passage, shoots after cold storage, and shoots developed from alginate-encapsulated buds (artificial seeds). All of these shoots showed the same ploidy level as seedlings obtained from the seeds (2C=8x=56), which served as a control. The results showed that shoots of R. chamaemorus cultured in vitro can be used for propagation and germplasm storage. Callus obtained from wounded generative embryos was mixoploid, consisting of cells with 2C, 4C and 8C DNA content. The estimated genome size of R. chamaemorus is 2C=2.46+/-0.05 pg.