Insect pests cause severe damage and yield losses from emergence to crop maturity. Insect pests also reduce lint quality by delaying maturity and infecting bolls with pathogens. Therefore, farmer must check field and identify any insect pests as well as beneficial insects if the field by following recommended pest scouting schedule and threshold. If certain insect pest has reached threshold, use of cultural and biological control must be considered. However, in some situations, the recommended insecticides must be applied as soon as possible.

Bt varieties only manage pink bollworms, fall army worm and to a certain extent may control some other caterpillars. However, other insect pest such as whitefly, aphid, thrips, and stink bugs are not controlled by Bt varieties. Therefore, insect pest control program must be planned very carefully based on recommended pest scouting schedule and specific insect pest infestation. In addition, Bt varieties may also need insecticide application due to increasing bollworm abundance and Bt resistance.