The increasing presence of glyphosate-tolerant weeds has increased the use of pre-emergence herbicides in cotton, Gossypium hirsutum L., grown in Tennessee during the last 5 to 8 years. These herbicides could have negative effects on seedling growth and potentially affect thrips (Thysanoptera: Thripidae) management or seedling disease with at-planting insecticides or fungicides. Experiments were conducted in 2013 and 2014 to evaluate the potential interactions of pre-emergence herbicides on the efficacy of insecticide or fungicide seed treatments in cotton. Nontreated plots and plots treated with a thiamethoxam seed treatment generally exhibited higher number of thrips, more thrips injury, less vigor, delayed maturity, and lower yields compared to plots treated with an imidacloprid seed treatment or an in-furrow application of aldicarb. Similarly, fungicide seed treatments generally reduced the incidence of seedling disease (primarily Rhizoctonia), while improving seedling health and stand density. Negative effects of some pre-emergence herbicides on plant health also were observed. For example, combination treatments of fluometuron plus S-metolachlor or fluometuron plus fomesafen reduced plant vigor and seedling biomass and there was a tendency for higher thrips populations where pre-emergence herbicides were used. There were no substantial interactions between injury caused by pre-emergence herbicides and that caused by thrips or seedling disease suggesting that thrips, seedling disease, and herbicide injury acted independently and additively. Following herbicide label rates should reduce the risk of compounding the effects of thrips or seedling disease with herbicide injury.