Low, non-freezing temperatures are a major factor limiting growth and development of vegetation in cold climates. Activation of the C-repeat binding factor (CBF) regulatory pathway by acute cold treatment is important for cold acclimation and freezing tolerance in Arabidopsis thaliana; however, the potential role of this pathway in response to chronic cold treatment has been less well characterised. We studied long-term (chronic) effects of low, non-freezing temperatures on the expression of CBF pathway genes (CBF2/3, COR15a, RD29A) and cell cycle-related genes (CDKA;1, CYCD2;1, CYCB1;1) in roots of accessions from habitats differing in growing season temperatures. Elongation rates of primary roots at 21 and 10 degrees C were not significantly correlated with average growing season temperatures, indicating that there is no ecotypic differentiation for these traits. Measurements of mRNA accumulation in roots of seven accessions showed that expression of CBF2/3, COR15a and RD29A is induced by both acute cold treatment (2-24 h at 4 degrees C) and chronic cold treatment (5-6 weeks at 10 degrees C), while CYCB1;1 is only induced by chronic cold treatment. RD29A and COR15a mRNA levels were correlated (P < 0.05) with the rate of root elongation in the cold for three high-altitude accessions relative to the common laboratory stain, Col-0. Our results are consistent with the hypothesis that induction of CBF2/3, COR15a, RD29A and CYCB1;1 is a physiological response to cold that, in the case of RD29A and COR15a, may be important for root growth at low temperatures.