Glucocorticoids are critical components of combination chemotherapy regimens in paediatric acute lymphoblastic leukaemia (ALL), although resistance is frequently encountered at relapse. Restoring glucocorticoid sensitivity could have a significant impact in improving disease outcome. The proapoptotic BIM protein is an important mediator of glucocorticoid-induced apoptosis in normal and malignant lymphocytes, while the antiapoptotic BCL2 confers resistance. The signalling pathways regulating BIM and BCL2 gene expression in glucocorticoid-treated lymphoid cells remain unclear. In this study, paediatric ALL patient-derived xenografts (PDXs) inherently sensitive or resistant to glucocorticoids were expanded and maintained in immunodeficient NOD/SCID mice. Eight hours following dexamethasone treatment of mice, human leukaemia cells were harvested from spleens. Microarray analysis showed that KLF13 and MYB gene expression changes were significantly greater in dexamethasone-sensitive than -resistant PDXs. ChIP analysis detected glucocorticoid receptor (GR) binding at the KLF13 promoter to trigger KLF13 expression only in sensitive PDXs. Next, KLF13 bound to the MYB promoter in competition with SP1, deactivating MYB expression only in sensitive PDXs. Sustained MYB expression in resistant PDXs resulted in maintenance of BCL2 expression and inhibition of apoptosis. ChIP-seq analysis revealed a novel GR binding site in a BIM intronic region (IGR) that was engaged only in dexamethasone-sensitive PDXs. Two conserved GR binding elements were identified at the BIM IGR and were shown to enhance BIM transcription in response to dexamethasone treatment by luciferase reporter assays. Analysing the abundance of DNaseI Hypersensitive Sites, we found that the BIM IGR exists in an open chromatin conformation exclusively in lymphoid cells, which indicates a critical role of chromatin conformation in glucocorticoid-induced apoptosis of lymphocytes. The absence of GR binding at the BIM IGR was associated with BIM silencing and dexamethasone resistance. This study has identified novel mechanisms of opposing BCL2 and BIM gene regulation that control glucocorticoid-induced apoptosis in paediatric ALL cells in vivo.