Single bud sets of nine varieties of sugar cane (Saccharum officinarum) hybrids, viz., CoLk 8102, CoLk 8001, CoS 767, CoLk 9617, CoLk 9606, CoS 95255, BO91, CoJ 64, and Co1148 were planted in soil tray culture conditions under natural cold (at 2-6 °C in the night and 10-16°C in the day from 25 December 2002 to 16 January 2003) and control conditions (25°C). Varieties CoJ 64, CoLk 9617, and CoS 95255 exhibited reduced rate of germination, while CoLk 9606, BO91 and CoS 767 showed higher rate of germination and early bud sprouting under low temperature. Average settling height decreased markedly in most varieties except CoS 767 and BO91 due to low temperature stress. Two varieties CoS 767 and BO91, that exhibited higher rates of germination were used to study the changes in isozyme pattern of catalases and peroxidases and protein profile. Peroxidase isozyme patterns showed one new isoform (Rm = 0.183) and higher intensity of most of the pre-existing isoforms of peroxidases. . Catalase isozymes showed higher expression in cold-affected leaves. Soluble protein profile of roots indicated high expression of 18 and 50 kDa proteins and new proteins of 75 and 60 kDa were synthesized in BO91 and CoS 767; 75 kDa protein was more marked in variety BO91. Results obtained showed genetic variability of germination behaviour of different varieties of sugar cane for tolerance against cold stress. Higher expression of catalases and peroxidases in leaves and synthesis of some new proteins in roots of cold-affected settlings may help in tolerance to chilling injury. This needs further exploration.