Abstract: Two cotton cultivars with different boron efficiency were cultured in pot experiments under boron deficient and sufficient conditions. Some physiological indexes concerning membrane lipid peroxidation and protection in cotton leaves were determined at seedling stage. When two cotton cultivars were suffered from boron deficiency, malonyl dialdehyde(MDA)content and membrane permeability in their leaves were increased, the activity of protective enzymes such as superoxide dismutase(SOD), peroxidase(POD) and catalase(CAT), the double bond index and the ratio of unsaturated to saturated fatty acid were decreased, however, the increase or decrease degree of boron efficient cultivar was less than that of inefficient one. The putrescine(Put) content was significantly reduced by boron deficiency in both cultivars, but with higher intensity in boron inefficient one. Boron deficiency caused a marked increase of the content of spermidine(Spd), spermine(Spm) and Spd+Spm+ Put in boron efficient cultivar, but only an upward trend in the inefficient cultivar. The results suggested that higher polyamines content in boron efficient cultivar under boron deficiency condition resulted in higher activity of protective enzymes, which might remain membrane function integrity.