Insect damage leads to changes in biochemical profile of plants. Response of three Brassica juncea-fruticulosa introgression lines (already reported resistant to Lipaphis erysimi) in terms of changes in biochemical constituents after aphid infestation was studied along with B. fruticulosa (resistant parent), B. juncea var. PBR −210 (susceptible parent) and B. rapa ecotype brown sarson BSH-1 (susceptible check). These six genotypes were grown under aphid infested and uninfested conditions and were sampled at peak aphid infestation to analyze the biochemical changes caused by aphid feeding from top 10 cm central twig of plant. A significant reduction in glucosinolates content in aphid infested plants of three introgression lines (I8, I79 and I82) was observed while opposite was observed in B. fruticulosa, PBR-210 and BSH-1. Exactly opposite trend was observed for total phenols where aphid infestation resulted in significant increase in phenols content in the three introgression lines while a decrease was observed in B. fruticulosa, PBR-210 and BSH-1. A general trend of decline in flavonols, total sugars and free amino acids content was observed after aphid infestation in all the genotypes. Glucosinolates and total phenols served as biochemical bases of resistance in the three introgression lines since there was downregulation of glucosinolates and upregulation of total phenols as against opposite trend observed in BSH-1 and PBR-210.