The G. hirsutum mutant li1 is caused by a dominant mutation which has pleiotropic effects on plant development. To get information for molecular effects by li1 mutation on cotton fiber development, we examined expression patterns of over 5000 genes by cDNA array from 6 to 18 DPA in a 3-day interval between li1 mutant and normal fibers. RNAs from li1 mutant fibers at 6-, 9-, 12-, 15-, and 18-DPA were compared to normal fiber RNA at each corresponding time points. Four biological repeats were carried out including two dye-swap ones.