Soil nitrogen (N) is available to rice crops as either nitrate or ammonium, but only nitrate can be accrued in cells and so factors that influence its storage and remobilization are important for N use efficiency (NUE). The hypothesis that the ability of rice crops to remobilize N storage pools is an indicator of NUE was tested. When two commonly grown Chinese rice cultivars, Nong Ken (NK) and Yang Dao (YD), were compared in soil and hydroponics, YD had significantly greater NUE for biomass production. The ability of each cultivar to remobilize nitrate storage pools 24 h after N supply withdrawal was compared. Although microelectrode measurements of the epidermal sub-cellular nitrate pools in leaves and roots showed similar patterns of vacuolar remobilization in both cultivars, whole-tissue analysis showed very little depletion of storage pools after 24 h. However, leaf epidermal cell cytosolic nitrate activities were significantly higher in YD when compared with NK. Before N starvation and growing in 10 mM nitrate, the xylem nitrate activity in YD was lower than that of NK. After 24 h of N starvation the xylem nitrate had decreased more in YD than in NK. Tissue analysis of stems showed that YD had accumulated significantly more nitrate than NK, and the remobilization pattern suggested that this store is important for both cultivars. Changes in nitrate reductase activity (NRA) and expression were measured. Growing in 10 mM nitrate, NRA was undetectable in roots of both cultivars, and the leaf total NRA of equivalent leaves was similar in NK and YD. When the N supply was withdrawn, after 24 h NRA in NK was reduced to 80% but no decrease was found in YD. The proportion of NRA in an active form in YD was significantly higher than that in NK under both nitrate supply and deprivation conditions. Checking NR gene expression showed that leaf expression of OsNia1 was faster to respond to nitrate deprivation than OsNia2 in both cultivars. These measurements are discussed in relation to cultivar differences and physiological markers for NUE in rice.