Tuberculosis (TB) is the second most common cause of death from infectious diseases. About 90% of those infected are asymptomatic - the so-called latent TB infections (LTBI), with a 10% lifetime chance of progressing to active TB. Several gene expression studies have compared healthy controls versus active TB or LTBI patients. The results vary due to diverse genetic background, study designs, and the inherent complexity of the disease process. Thus, developing a sensitive and efficient method for the detection of LTBI is both crucial and challenging. Our objective was to establish an efficient and cost-effective pipeline for gene and microRNA expression profiling in TB and LTBI. We attempted to investigate the interaction between these two types of molecular signatures as biomarkers for a more sensitive and specific differentiation among active TB, LTBI, and healthy individuals. Following our systematic pipeline, we have uncovered novel differences specific to the Taiwanese population. Differentially expressed microRNAs and their interactions with the corresponding target genes will serve as potential molecular signatures to enhance our understanding of the underlying mechanisms of TB and facilitate the development for a more sensitive diagnostic assay for LTBI.