An experiment was carried out for two years in a greenhouse to study the effect of fungicides treatment on the germination of seeds of São Paulo cotton varieties, IAC 13-1 and IAC 17. Treated seeds were stored in uncontrolled conditions and germination was tested yearly. For each variety, the following treatments were applied: 1) PCNB + thiram, 2) Benomyl, 3) Check (mechanically delinted seed), 4) Acid delinted seed (D.A.), 5) D.A. + PCNB + thiram, 6) Metallic mercury. For treatments 1, 2 and 6 mechanically delinted seeds were used. Germination tests were carried out, in a randomized block design with three replications, by using fifty seeds in each experimental plot. Results were avaliated through an emergence index (%) and a resistance index (%) and showed the following: 1) The fungicide metallic mercury, PCNB + thiram, and Benomyl, had a significant effect on germination seven months after treatment, that persisted after sixteen months, except for Benomyl treatment. 2) The acid delinted seeds showed a decrease in germination at the sixteen months test. However, the negative effect of this treatment was adding PCNB + thiram.