This paper provided reasonable results of groundwater storage estimation and its distribution on each aquifer in Uzbekistan. The largest aquifer was Kyzylkum. There were very rare publication and discussion paper on the groundwater storage in arid region. Then the results were useful finding to support the decision maker and researchers who were interested in this subject. In this study, the estimation of groundwater storage using GIS techniques and utilization of borehole data was proposed. The result showed that groundwater storage in Uzbekistan was about 15.5 BCM (billion cubic meters), while in Kyzylkum aquifer was about 6.8 BCM. Compared with the result from Central Asia Water Info, field survey and roundtable discussion Uzbekistan on August 2007, the results was verified, reliable and acceptable.