A better understanding of genomic region might provide a genetic basic for the improvement of nitrogen use efficiency (NUE). The objective of this study was to identify the genetic regions affecting NUE in rice through the study of contrast cultivars and recombinant inbred lines (RILs) for QTLs analysis. A total of 169 RILs and their parents IR64 and Azucena were cultivated in the same conditions under different nitrogen conditions in two separated experiments. The WinQTL Cartographer version 2.5 was used to analyze joint QTL for multiple traits of each experiment. The first mapping experiment showed a total of 44 QTLs for all 15 observed parameters including number of leaves (NL), number of tillers (NT), plant height (PH), total fresh matter (FM), dry weight of roots (DWR), dry weight of leaf sheaths plus stems (DWS), dry weight of leaf blades (DWL), total dry matter (DM), chlorophyll content index (CCI), N concentration in roots (%NR), N concentration in leaf sheaths plus stems (%NS), N concentration in leaf blades (%NL), absorption NUE (aNUE), physiological NUE (pNUE) and agronomical NUE (agNUE) on chromosome 1, 2, 3, 4, 5, 6, 7, 8, 10 and 12. The second experiment detected 44 QTLs for NL, NT, PH, FM, DWR, DWS, DWL, DM, CCI, %NR, %NL, aNUE and agNUE on chromosome 1, 2, 3, 5, 6, 7, 8 and 12.