Provided are methods of increasing nitrogen use efficiency, yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality and/or abiotic stress tolerance of a plant by expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least 80% identical to SEQ ID NO: 387, 1-386, 388-469, 763-3704 and 3705; or an exogenous polynucleotide encoding a polypeptide at least 80% identical to SEQ ID NO: 602, 470-601, 603-762, 3706-5858, 5860-5910, 5912, 5914-5923, 5925-6046 or 6047. Also provided is an isolated polynucleotide comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 387, 1-386, 388-469, 763-3704 and 3705, which can be used to increase the nitrogen use efficiency, yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality and/or abiotic stress tolerance of a plant.