Experiments were carried out to study changes in the physiological and biochemical properties of cotton seedling roots with respect to high temperature and waterlogging treatments. It to clear from these, studies that both high temperature and waterlogging significantly damaged the seedling roots and affected their physiological and biochemical activities. Cultivars showed no effect an their root growth for heat stresses up to 30'C but were adversely affected when stressed above this temperature. Cultivar MIN-93 performed well up to about 38'C, while Qalandari showed an inhibition at temperatures of 35 *C and above. At a temperature of 45 C, roots of both cultivars were Irreparably damaged. When careful statistical analysis of the data was carried out. however. no significant differences were found between the cultivars studied. Fresh weight and dry weight values were only determined for MR-93, but they confirmed the findings of the root growth measurements for that cultivar. Stress temperatures above 40*C caused a loss of phospholipids. The results of (MO_14 C) choline incorporation studies revealed that each of four cultivare showed different rates of incorporation into PC under normal germinating conditions at 25'C. Longer roots incorporated more (Me- 14C) choline than shorter roots. At temperatures of 40*C and above, (Me_14 C) choline incorporation decreased with increasing temperature. At 50 C, more than 802 of the activity was lost in all the four cultivars studied. in general, no significant differences were found between the cultivars studied. The results of fatty acid analyses suggested that greater unsaturation occurred with increasing germination time. High temperature had a marked effect on fatty acid composition and caused significant changes especially in neutral lipid and glycolipid fatty acids. Small changes were also observed in phospholipid fatty acids. A large increase of free fatty acids was found in MM-93 but not In S-12 at the end of recovery following heat shock. In this respect, the cultivar 5-12 appeared to be a relatively better cultivar than MNH-93, since free fatty acids are known to be damaging to cells. Waterlogging had significant effects on root growth in all the four cultivars studied. Increasing waterlogging time caused greater damage to the root system and waterlogging for 24 hours stopped further root growth completely. In terms of both root growth and visible damage, S-12 was clearly a more tolerant cultivar than KKK-93, Rehmani or Qalandari. Aerated waterlogging caused smaller reductions in root growth in two cultivars studied (Qalandari and S-12). In this treatmwnt, no visible damage to the roots was seen. Waterlogging also caused large reductions in respiratory activities. During recovery following waterlogging treatments, Qalandarj recovered its r*spiratory activity such faster than the cultivar S-12, however. in this respect, Qalandari appeared to be a more tolerant cultivar than S-12. Patty acid analyses following waterlogging showed changes in both their levels and their relative composition. This treatmmt caused a marked Increase in the amount of esterified fatty acids. Waterlogging also enhanced the synthesis of a set of low molecular weight compounds and suppressed the synthesis of all the "normal" fatty acids. A significant increase in free fatty acids was observed in MNH-93 but not in 3-12. This particular met of results suggests that 5-12 was & rolatively better cultivar than the "NU-93. When taken altogether, the results suggested that there in very little genetic variability between the cultivars of cotton commonly grown in Pakistan with respect to beat tolerance and waterlogging tolerance.