Malondialdehyde (MDA) is a naturally occurring product of lipid peroxidation and the level of MDA in plant is often used as a parameter to evaluate the damage to plants' cells due to stress. Plant with lower amounts of MDA under drought conditions is generally considered as more tolerant to drought. In this study, a population of recombinant inbred lines was used to map the quantitative trait locus (QTLs) that controlled MDA content under well-watered condition (WW) and water deficit (WD) condition. A major QTL, designated as Qheb.mda-3B, was detected on the long arm of chromosome 3B. Based on interval mapping analysis, Qheb.mda-3B explained 31.5 and 39.0% of the phenotypic variance under WW and WD conditions, respectively. Qheb.mda-3B was located in the same interval as a previously identified QTL (Qcrs.cpi-3B) that controlled resistance to Fusarium crown rot (FCR), a fungal disease caused by Fusarium species. Three pairs of near-isogenic lines (NILs) previously developed for Qcrs.cpi-3B were found to show significant differences in MDA content under WD condition. These results suggested that same set of genes is likely to be involved in drought tolerance and FCR resistance in wheat.