The present invention relates to vesicles derived from the genus Bacillus bacteria and a use thereof. The present inventors have confirmed that the vesicles are significantly reduced in samples of patients with cancers, such as liver cancer, bladder cancer, breast cancer, and ovarian cancer; inflammatory diseases, such as asthma and atopic dermatitis; or metabolic diseases, such as diabetes and cirrhosis, compared with normal persons, and the vesicles inhibited the secretion of inflammatory mediators by pathogenic vesicles, such as. coli-derived vesicles, which are causative factors of inflammatory diseases, diabetes, and the like. Therefore, the vesicles derived from the genus Bacillus bacteria according to the present invention can be advantageously used for the purpose of developing a diagnostic method for cancer, inflammatory diseases, and metabolic diseases, and a preventive or therapeutic composition therefor.