Due to the physico-chemical similarities of caesium (Cs(+)) to potassium (K(+)) on the one hand and strontium (Sr(2+)) to calcium (Ca(2+)) on the other hand, both elements can easily be taken up by plants and thus enter the food chain. This could be detrimental when radionuclides such as (137)Cs and (90)Sr are involved. In this study, both genetic and physiological aspects of Cs(+) and Sr(2+) accumulation in Arabidopsis thaliana were investigated using 86 Arabidopsis accessions and a segregating F(2) population of the low Cs(+) accumulating Sq-1 (Ascot, UK) crossed with the high uptaking Sorbo (Khurmatov, Tajikistan). Hydroponically grown plants were exposed to subtoxic levels of Cs(+) and Sr(2+) using radioactive isotopes as tracers. In the natural accessions shoot concentration of Cs(+) as well as Sr(2+) varied about 2-fold, whereas its heritability ranged for both ions between 0.60 and 0.73. Shoot accumulation of Cs(+) and Sr(2+) could be compromised by increasing concentrations of their essential analogues K(+) and Ca(2+), respectively, causing a reduction of up to 80%. In the case of the segregating F(2)/F(3) population Sq-1×Sorbo, this study identified several QTL for the trait Cs(+) and Sr(2+) accumulation, with main QTL on chromosomes 1 and 5. According to the correlation and discrimination surveys combined with QTL-analysis Cs(+) and Sr(2+) uptake seemed to be mediated mostly via non-selective cation channels. A polymorphism, affecting amino acids close to the K(+)-pore of one candidate, CYCLIC-NUCLEOTIDE-GATED CHANNEL 1 (CNGC1), was identified in Sorbo and associated with high Cs(+) concentrating accessions.