Autosomal recessive polycystic kidney disease (ARPKD) is one of the most common hereditary renal cystic diseases in children. The clinical spectrum ranges from stillbirth and neonatal demise to survival into adulthood. In a given family, however, patients usually display comparable phenotypes. Many families who lost a child with severe ARPKD desire an early and reliable prenatal diagnosis (PD). Given the limitations of antenatal ultrasound, this is only feasible by molecular genetics that became possible in 1994 when PKHD1, the locus for ARPKD, was mapped to chromosome 6p. However, linkage analysis might prove difficult or even impossible in families with diagnostic doubts or in whom no DNA of an affected child is available. In such cases the recent identification of the PKHD1 gene provides the basis for direct mutation testing. However, due to the large size of the gene, lack of knowledge of the encoded protein's functional properties, and the complicated pattern of splicing, significant challenges are posed by PKHD1 mutation analysis. Thus, it is important to delineate the mutational spectrum and the reachable mutation detection rate among the cohort of severely affected ARPKD patients. In the present study, we performed PKHD1 mutation screening by DHPLC in a series of 40 apparently unrelated families with at least one peri- or neonatally deceased child. We observed 68 out of an expected 80 mutations, corresponding to a detection rate of 85%. Among the mutations identified, 23 were not reported previously. We disclosed two underlying mutations in 29 families and one in 10 cases. Thus, in all but one family (98percnt;), we were able to identify at least one mutation substantiating the diagnosis of ARPKD. Approximately two-thirds of the changes were predicted to truncate the protein. Missense mutations detected were nonconservative, with all but one of the affected amino acid residues found to be conserved in the murine ortholog. PKHD1 mutation analysis has proven to be an efficient and effective means to establish the diagnosis of ARPKD. Hum Mutat 23:487–495, 2004. © 2004 Wiley-Liss, Inc.