The objective of this study was to explore the effects of ultrasound probe diameter, reactor diameter, and juice level in the reactor upon effectiveness of ultrasound waves on decontamination of sour cherry juice. Results showed that the effects of probe diameter, reactor diameter and reactor height were significant (P<0.01). In addition, by increasing the probe diameter from 30 to 40 mm no significant effect was seen in reactors with 65 and 75 mm diameter; however, for 85 mm diameter reactor, the effect of ultrasound waves diminished and, as a result, the total microbial count increased. Increasing the probe diameter from 20 to 30 and then 40 mm, on the average decreased the total microbial count by 15% and 5%, respectively. This effect was obvious at 85 mm diameter, and any increase in height steepened the slope of total microbial count. Finally, using the response surface method (RSM), optimum values were obtained for reactor diameter, reactor height, and probe diameter.