The levels of three endogenous cytokinin equivalents: zeatin (Z), iso-pentenyladenine (iP) and dihydrozeatin (dZ) in two Arabidopsis thaliana (L.) Heynh genotypes — wild type (wt) and ethylene-insensitive mutant (eti5), were compared using enzyme immunoassay (ELISA). Cytokinin content was measured after exposure to low (4 °C for 24 h in darkness) or high temperature (38 °C for 24 h in darkness). Measurements were performed immediately and 24, 48 and 120 h after treatments. It was found that at normal growth conditions eti5 plants contained more endogenous cytokinins compared to the wild type. At both temperature treatments mutant plants had decreased total cytokinin levels. Wild-type plants treated with high temperature (HT) exhibited reduced total cytokinins (with the exception of rates at 48 h), while low temperature (LT) treatment resulted in elevated total amount of the studied equivalents (except at 24 h). The obtained results suggested that HT had greater effect on cytokinin levels than LT since it caused more profound changes in the total content. We assume that this was due to the natural chilling tolerance of Arabidopsis plants.