Leptospirosis is a bacterial zoonosis of global importance, caused by Leptospira. The incidence of disease leading to one million severe cases and 60,000 deaths per year. Despite considerable advances in research, much is yet to be discovered about disease pathogenicity. The influence of epigenetic mechanisms, particularly RNA-mediated post-transcriptional regulation of host immune response has been proven vital following a variety of bacterial infections. The aim of this study was to identify and characterize, for the first time, the influence of miRNAs on the regulation of the immune response to Leptospira infection. We examined the microtranscriptome, trough microarray technique, of macrophages J774A.1 following an 8h infection with virulent, attenuated and saprophyte strains of Leptospira. Microarray analysis revealed that 29 miRNAs were de-regulated by the Leptospira strains compared to control with fold change ±1.5 and p-value <0.01. Enrichment analyses of the targets of these differentially expressed miRNAs suggest that several processes involved in immune response are directly regulated by miRNAs. We suggest that posttranscriptional regulation by miRNAs may play a role in host response to infection in leptospirosis, and that this response is dependent on species and bacterial virulence.