Whole-genome sequence analysis of Mycobacterium leprae has revealed a limited number of protein-coding genes, with half of the genome composed of pseudogenes and noncoding regions. We previously showed that some M. leprae pseudogenes are transcribed at high levels and that their expression levels change following infection. In order to clarify the RNA expression profile of the M. leprae genome, a tiling array in which overlapping 60-mer probes cover the entire 3.3-Mbp genome was designed. The array was hybridized with M. leprae RNA from the SHR/NCrj-rnu nude rat, and the results were compared to results from an open reading frame array and confirmed by reverse transcription-PCR. RNA expression was detected from genes, pseudogenes, and noncoding regions. The signal intensities obtained from noncoding regions were higher than those from pseudogenes. Expressed noncoding regions include the M. leprae unique repetitive sequence RLEP and other sequences without any homology to known functional noncoding RNAs. Although the biological functions of RNA transcribed from M. leprae pseudogenes and noncoding regions are not known, RNA expression analysis will provide insights into the bacteriological significance of the species. In addition, our study suggests that M. leprae will be a useful model organism for the study of the molecular mechanism underlying the creation of pseudogenes and the role of microRNAs derived from noncoding regions.Mycobacterium leprae, the causative agent of leprosy, cannot be cultivated in vitro. Therefore, bacteriological and pathological information, such as the mechanisms of infection, parasitization, and replication, are still largely unknown. However, whole-genome sequencing has provided insight into many biological characteristics of M. leprae (5). The M. leprae genome consists of 3.3 Mbp, which is much smaller than the 4.4 Mbp of the Mycobacterium tuberculosis genome. M. leprae has 1,605 genes and 1,115 pseudogenes, while M. tuberculosis has 3,959 genes and only 6 pseudogenes. The number and ratio of pseudogenes in M. leprae are exceptionally large by comparison with the pseudogene numbers and ratios for other pathogenic and nonpathogenic bacteria and archaea (21). A feature of M. leprae pseudogenes is the massive fragmentation caused by many insertions of stop codons (26). The functional roles, if any, of these unique pseudogenes and noncoding regions are unknown. However, we have shown that some M. leprae pseudogenes are highly expressed as RNA and that their expression levels change following macrophage infection (36). In that study, a membrane-based DNA array was created utilizing a cosmid DNA library that covered Ͼ98% of the M. leprae genome. mRNAs purified from M. leprae-infected macrophages and control bacilli were enriched by cDNA subtraction and hybridized to these arrays. Southern blot analysis of the positive cosmid clones identified 12 genes that might be important for the survival and infection of M. leprae.