In the present study fifty genotypes of Brassica juncea were evaluated for heat stress tolerance in terms of biochemical components, in four day old seedlings. Heat shock was given at 45 degrees C for 4.5 hr and thereafter survival percentage, electrolyte leakage and chlorophyll content were estimated. Tolerant genotypes (10) registered survival greater than 65%, moderately tolerant (20) between 35-65% and susceptible (20) less than 35%. Electrolyte leakage was significantly (p < 0.001) higher in susceptible genotypes than in tolerant ones with respect to control seedlings. Chlorophyll content showed no significant variation among the tolerant, moderately tolerant and susceptible genotypes, although it registered a decline in response to heat stress. Lipid peroxidation, assessed by malondialdehyde (MDA) in stressed conditions was 4.66 (MDA g(-1) f. wt. of tissue) in tolerant genotypes, 7.44 (MDA g(-1) f. wt. of tissue) in susceptible genotypes and correlated significantly (r = 0.563) with electrolyte leakage. Increase in POD activity under heat stress was maximum in tolerant class with respect to control. CAT activity showed decrease after heat shock treatment in all the three classes but the decrease was 1.3 fold in tolerant genotypes as compared to 1.6 fold in susceptible genotypes. The non-enzymatic antioxidants glutathione and proline registered a significantly (< 0.01) high value in tolerant genotypes on heat shock treatment in comparison to susceptible genotypes corroborating the role of antioxidants in mitigating the effect of heat stress in Bjuncea. The antioxidants and proline seemed to play role in mitigating the effect of heat stress.