Glioblastoma, the most aggressive and malignant form of glioma, appears to be resistant to variouschemotherapeutic agents. Hence, approaches have been intensively investigated to targeti specific molecularpathways involved in glioblastoma development and progression. Aloe emodin is believed to modulate theexpression of several genes in cancer cells. We aimed to understand the molecular mechanisms underlying thetherapeutic effect of Aloe emodin on gene expression profiles in the human U87 glioblastoma cell line utilizingmicroarray technology. The gene expression analysis revealed that a total of 8,226 gene alterations out of 28,869genes were detected after treatment with 58.6 μg/ml for 24 hours. Out of this total, 34 genes demonstratedstatistically significant change (p<0.05) ranging from 1.07 to 1.87 fold. The results revealed that 22 genes wereup-regulated and 12 genes were down-regulated in response to Aloe emodin treatment. These genes were thengrouped into several clusters based on their biological functions, revealing induction of expression of genesinvolved in apoptosis (programmed cell death) and tissue remodelling in U87 cells (p<0.01). Several genes withsignificant changes of the expression level e.g. SHARPIN, BCAP31, FIS1, RAC1 and TGM2 from the apoptoticcluster were confirmed by quantitative real-time PCR (qRT-PCR). These results could serve as guidance forfurther studies in order to discover molecular targets for the cancer therapy based on Aloe emodin treatment.