Mycobacterium leprae, the etiological agent of leprosy, is noncultivable on axenic media. Therefore, the viability of M. leprae for clinical or experimental applications is often unknown. To provide new tools for M. leprae viability determination, two quantitative reverse transcriptase PCR (RT-PCR) assays were developed and characterized. M. leprae sodA mRNA and 16S rRNA were used as RNA targets, and M. leprae repetitive element (RLEP) DNA was used to determine relative bacterial numbers in the same purified bacterial preparations or from crude biological specimens. Results demonstrated that both assays were good predictors of M. leprae viability during short-term experiments (48 h) involving rifampin (rifampicin) treatment in axenic medium, within rifampin-treated murine macrophages (M⌽), or within immune-activated M⌽. Moreover, these results strongly correlated those of other M. leprae viability assays, including radiorespirometry-based and Live/Dead BacLight viability assays. The 16S rRNA/RLEP assay consistently identified the presence of M. leprae in eight multibacillary leprosy patient biopsy specimens prior to multidrug therapy (MDT) and demonstrated a decline in viability during the course of MDT. In contrast, the sodA/RLEP assay was able to detect the presence of M. leprae in only 25% of pretreatment biopsy specimens. In conclusion, new tools for M. leprae viability determination were developed. The 16S rRNA/RLEP RT-PCR M. leprae viability assay should be useful both for short-term experimental purposes and for predicting M. leprae viability in biopsy specimens to monitor treatment efficacy, whereas the sodA/RLEP RT-PCR M. leprae viability assay should be limited to short-term experimental research purposes.Leprosy is a chronic infectious disease of skin and peripheral nerves and is of special concern because it can progress to peripheral neuropathy and permanent progressive deformity. Despite a marked reduction in the prevalence of leprosy since the implementation of multidrug therapy (MDT), the detection rate for new cases has not shown a substantial decline (2). One explanation is that standard immunological and histological approaches for disease assessment are less effective in the diagnosis of early leprosy, and therefore, disease and transmission can progress. In addition, in vitro Mycobacterium leprae viability assays such as those based on radiorespirometry (RR) and the Live/Dead BacLight fluorescent bacterial viability assay require large quantities of bacteria, 10 7 and 10 6 bacteria, respectively, for reliable detection and are therefore not applicable for direct detection in clinical specimens (14, 28). The bacterial index (BI) is a long-established method for monitoring the patients' responses to chemotherapy by giving an estimation of the number of acid-fast bacilli present in skin smears of lesions and other specific sites of the skin of leprosy patients. The BI range is 1 to 6, where 1 is the least amount of bacilli detectable and 6 is the most. However, the BI drops very slowly during t...