Nephronophthisis (NPHP) is the most common genetic cause of kidney failure in children. Ten causative genes (NPHP1-NPHP9 and NPHP11), all of which generate proteins that localize to a cellular complex known as the primary cilia-centrosome complex, have been identified previously. Researchers recently analyzed an association between mutations in the XPNPEP3 gene and an NPHP-like nephropathy in two consanguineous families, one in northern Finland and one in Turkey. Unlike all the known NPHP proteins, XPNPEP3 protein localizes to cellular compartments known as mitochondria. However, in vivo analysis in zebrafish indicated that XPNPEP3 protein has a role in ciliary function, as it degraded several ciliary cystogenic proteins. The researchers conclude that there is a link between mitochondria and ciliary dysfunction, a key component of NPHP. These data provide exciting new avenues of research for understanding ciliopathies, genetic disorders caused by damage to cellular structures known as primary cilia.