In recent years, the serpentine leaf miner Liriomyza trifolii (Burgess) has become a major pest of cotton (Gossypium spp.) in India, with high levels of incidence observed at the seedling stage, particularly in transgenic Bt cotton. We monitored the severity of infestation and damage by L. trifolii to transgenic and non-transgenic genotypes of Gossypium arboreum L. and G. hirsutum L. between 2002 and 2007. Overall, significantly lower L. trifolii damage occurred in G. arboreum varieties than in G. hirsutum varieties and hybrids. Among the G. hirsutum genotypes, damage was significantly lower in varieties than in hybrids. However, no significant differences in damage were observed between Bt and non-Bt cotton hybrids. Abiotic factors had a major influence on the severity of damage; there was a significant and negative association of L. trifolii damage with open pan evaporation (E), maximum temperature, solar radiation and sunshine, and a significant and positive association with relative humidity and rainfall (RF). Multiple stepwise regression analysis indicated that 99% of the variation in L. trifolii damage was accounted for by RF, open pan E and relative humidity.