Mitochondrial respiratory chain disorders (MRCD) are rare diseases that affect multiple organs with varying severity. MRCD can be caused by mutations in mitochondrial or nuclear genes. At present, approximately 250 nuclear genes have been identified as candidates for MRCD. However, the pathogenic mechanisms of MRCD are not fully understood. Model organisms provide unique opportunities to study molecular basis of human diseases. The fruit fly, Drosophila melanogaster is one of the best model organisms, in which one can utilize advanced knowledge and techniques of genetics, and a large number of resources, such as mutant stocks, and cDNA collections. Here, we established Drosophila models of MRCD through knocking down the orthologs of 13 human MRCD candidate genes identified in Saitama Medical University. We used the Gal4/UAS system-mediated transgenic RNAi to produce knockdown (KD) flies for each candidate gene, and analyzed MRCD-related phenotypes. Among the candidate genes (MRCD1-13), MRCD11-KD flies exhibited remarkable phenotypes: reduced body size and severe defects in locomotor activity, respiratory dysfunction and short lifespan. In addition, biochemical analysis revealed that they have symptoms of lactic acidosis and mitochondrial respiratory chain complex I defects which were similar to symptoms of the MRCD patient. These results suggested MRCD11 gene is a causative gene for MRCD. MRCD11-KD flies should be useful as a model to investigate the role of the gene and to understand the molecular pathogenesis of MRCD.