Autosomal dominant polycystic kidney disease (ADPKD) is the most common renal hereditary disorder. Clinical expression of ADPKD shows interfamilial and intrafamilial variability. We screened for mutations the 3' region of the PKD1 gene, from exon 43 to exon 46, in a family showing anticipation and Caroli's disease and have found a 28 base pairs deletion in exon 46 (12801del28) and a new DNA variant in exon 43 (12184 C to G conserving Ala 3991) segregating with the disease. The mutation should result in a protein 44 amino acids longer then the wild-type PKD1. This PKD1 mutation manifests as typical adult-onset disease in the father, but in the proband, a 26-year-old man, ADPKD was diagnosed as a newborn and was associated with Caroli's disease at the age of 18 years. A renal biopsy performed in childhood disclosed a predominance of glomerular cysts. Mutation 12801del28 is the first molecular defect associated with Caroli's disease and the PKD1 phenotype. The finding of the same mutation in two different members of the same family with different expression of the disease indicates that the phenotypic variation in ADPKD must be due to modifying factors that may radically affect the course of the disease.