We examined the gene expression of human leukemia Molt-4 cells treated with non-thermal low intensity pulsed ultrasound. Six hours after 0.3W/cm(2) pulsed ultrasound treatment, apoptosis (24+/-3.3%, mean+/-SD) with minimal cell lysis was observed. Of approximately 16,600 genes analyzed, BCL2-associated athanogene 3 (BAG3), DnaJ (Hsp40) homolog, subfamily B, member 1 (DNAJB1), heat shock 70 kDa protein 1B (HSPA1B), and heat shock 70 kDa protein 6 (HSPA6) showed increased levels of expression while isopentenyl-diphosphate delta isomerase (IDI1) and 3-hydroxy-3-methylglutaryl-coenzyme A synthase 1 (HMGCS1) showed decreased levels in the cells 3h after the ultrasound treatment. The expression levels of these six genes were confirmed by a real-time quantitative polymerase chain reaction. To our knowledge, this is the first report of DNA microarray analysis of genes that are differentially expressed in response to apoptosis induced by non-thermal low intensity pulsed ultrasound in human leukemia cells. The present results will provide a basis for further understanding of the molecular mechanisms of effects of not only low intensity pulsed ultrasound but also that of mechanical shear stress in the cells.