Using the regeneration method described by Feldman and Marks (1986), the level of somaclonal variation (frequency of gene mutations and chromosomal changes) was determined in A. thaliana regenerants from root and shoot explants. The explants were regenerated via indirect organogenesis with callus stage. The level of embryo lethal mutations and changes in chromosome number were estimated in R2 generative progeny of regenerants, and confirmed in R3 generation. The frequency of R1 plants carrying gene mutations was similar for all types of explants and on average it reached 8.3%, however only 47% of R1 plants showed the presence of the same embryo mutation in R2 and R3 generation. The frequency of embryo-lethal mutants, among 25 571 embryos tested, was 1.7%, while 0.08% embryos carried chlorophyll mutations. The plants with increased chromosome number were observed in the progeny of 32.2 % R1 regenerants, i.e. with eight times higher frequency than regenerants carrying gene mutations. All polyploid plants were obtained from shoot explants, while regenerants from roots carried normal diploid number of chromosomes. The observed changes in chromosome number were discussed in relation to the different content of DNA in root and shoot cells of A. thaliana.