It was evaluated the effect of alachlor and pendimethalin herbicides in the doses zero (control), 12.5, 25, 50 and 100mg.ml-1 on fungi present in cotton seeds (IAC 22 cultivar), harvested in 1995/96. Seeds were plated on three blotters (80g/m2) wetted with the herbicides in the respective doses within plastic Petri dishes. Control was wetted with distiled and sterilized water. The experimental plot was 200 seeds and the trial was carried out in randomized plots in four replications. The seeds were incubated at 20±2°C for seven days with 12 hours photoperiod. The following identified fungi allowed statistical analysis: Colletotrichum gossypii, Botryodiplodia theobromae and Fusarium spp. The results showed significant effect among doses and fungi. Among the herbicide there was difference, but they decreased the percentage of fungi in cotton seeds.