AbstractAutosomal recessive polycystic kidney disease (ARPKD) is an often devastating form of polycystic kidney disease that presents primarily in infancy. The locus,PKHD1(polycystic kidney and hepatic disease 1), on chromosome 6p21.1–p12, has been linked to all classical forms of this disorder. In previous studies, we cloned thePKHD1interval in a set of overlapping YACs, converted this YAC‐based framework into a BAC/PAC contig, and delimited the critical interval to a region flanked by the markersD6S1714andD6S1024. We now have refined the genetic interval using new polymorphic markers developed from our BAC/PAC resources. In addition, we have evaluated a recently identified, EF hand‐containing gene that maps to the interval of interest, established its transcript sequence, defined its genomic organization, and excluded this new gene as aPKHD1candidate. Therefore, this study has narrowed thePKHD1interval and excluded a potentially relevant gene as aPKHD1candidate gene. This further refinement of thePKHD1interval will facilitate efforts to identify thePKHD1gene by positional cloning. These data also provide additional, highly polymorphic markers for haplotype‐based diagnostic testing for ARPKD. © 2002 Wiley‐Liss, Inc.