Objective: To analyse the expression of differential mRNA in the plasma exosomes in patients with latent tuberculosis infection (LTBI) and active tuberculosis (ATB) using high-throughput sequencing, so as to provide insights into differential diagnosis of LTBI and ATB. Methods: The plasma samples were collected from the patients treated at The Affiliated Hospital of Hangzhou Normal University, including 16 cases of LTBI and 21 cases of ATB. The exosomes were extracted by Invitrogen extracellular extracts purification kit, and the size and morphology of exosomes were observed by transmission electron microscope (TEM). The exosomes were identified by Western blotting. Total RNA was extracted from plasma exosomes using high-throughput sequencing, differential expression mRNA was identified, and gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Two differential mRNAs with the highest differential expression fold were selected, and five patients with ATB and three patients with LTBI were recruited for verification using real-time quantitative PCR. Results: The sequencing results of plasma exosomes showed that compared with ATB patients, 2 875 differentially expressed mRNAs were detected in exosomes of LTBI patients, of which 1 002 mRNAs were up-regulated and 1 873 mRNAs were down-regulated. The most significant differentially expressed downregulated and upregulated mRNA were M6PR and RGPD5, respectively. GO analysis and KEGG pathway analysis showed that differential mRNAs were enriched in protein serine kinase activity, rRNA binding molecular function, human cytomegalovirus infection, pancreatic cancer, endometrial cancer, insulin signaling pathway and FoxO signaling pathway. The real-time quantitative PCR showed that the expression of differential mRNA was consistent with sequencing. Compared with ATB patients, the relative expression level of M6PR in plasma exosomes in LTBI patients (0.954±0.212) was downregulated compared with that of ATB patients (2.168±0.226), while the relative expression level of RGPD5 (2.126±0.200) was upregulated compared with that of ATB patients (0.588±0.129) (both P<0.05). Conclusions There is a difference in mRNA expression of plasma exosomes between patients with LTBI and ATB. M6PR and RGPD5 may become markers for distinguishing plasma exosomes between LTBI and ATB.