RNA-seq is a more effective method for identifying significant changes in the levels of microRNAs between healthy people and individuals with active disease and for identifying microRNAs with potential as biomarkers for TB diagnosis. Here, we identified and quantified the expression of a total of 904 microRNAs in serum from four experimental groups, namely individuals with active TB, individuals with latent TB infections, and healthy individuals, with or without prior BCG inoculation. Identification of biomarkers which can discriminate between latent TB infection and active TB disease is one of the most important issues in TB prevention and control. Recently, several studies on differences in the levels of microRNAs between patients with active TB and individuals with latent TB infection have been reported. Here, we have tried to identify further microRNAs that are specific and can be used to discriminate between the four experimental groups. We identified 24 microRNAs that are R428 1037624-75-1 up-regulated and 6 that are downregulated in active TB patients compared with the three groups of healthy controls. Our results confirm the potential of hsa-miR-29a, and hsa-miR-22 as biomarkers in TB diagnosis. We have also identified other microRNAs which can discriminate between active TB patients and latently-infected individuals; 59 miRNAs were down-regulated and 33 miRNAs were up-regulated in patients with active disease. In addition to the greater sensitivity of RNA-Seq for the detection of microRNAs, the inclusion of three control groups in this study increases the accuracy of identifying markers that are genuinely associated with active disease. BCG inoculation is routinely performed on new-born babies throughout most regions in China. The development of an easy method for discriminating between BCG-inoculated individuals and those with latent TB infections is thus of great importance. To that end, we included the detection of microRNA in the serum of BCG-inoculated individuals in our study. Results showed that 83 microRNAs were up-regulated and 11 were down-regulated in LTBI individuals in comparison with BCG-inoculated individuals. We provide evidence here for the first time that a significant change in the levels of microRNAs occurs in the serum of latent TB infected individuals relative to BCG-inoculated individuals. Many differentially-expressed miRNAs, such as the four microRNAs validated here using qRT-PCR, are involved in inflammation. Hsa-miR-516b, hsa-miR-486-5p and hsa-miR-376c all target NFAT5. Hsa-miR-486-5p is associated with cancers, such as lung cancer, gastric cancer,and neuroblastoma. Hsa-mir-196b, first reported in 2004, inhibits proliferation and induces apoptosis in endometriotic stromal cells and is associated with cervical tumours. Hsa-miR-376c, first reported by Sylvius et al is associated with muscular dystrophy.