Early and severe forms of polycystic kidney disease (PKD) do already manifest during childhood or adolescence. They are characterized by enlarged kidneys and diminished renal function that prenatally may result in Potter's oligohydramnios sequence. Genetically, various defects can mimic this phenotype. Most common are PKHD1 mutations that lead to autosomal recessive PKD (ARPKD). About the same number of children do carry mutations in the dominant autosomal dominant polycystic kidney disease (ADPKD) genes, PKD1 and less frequent PKD2, often arise de novo or may affect both disease alleles in a recessive mode. Mutations in DZIP1L have been recently described to result in an ARPKD-like phenotype. Likewise, mutations in several other cystogenes can phenocopy early and severe PKD. Early and reliable prenatal diagnosis for which there is a strong demand in ARPKD and related diseases is feasible only by genetics. A comprehensive knowledge of disease-causing genes is essential for the correct diagnosis and parental counselling. The increasing number of genes that need to be considered benefits from the advances of next generation sequencing and allows the simultaneous analysis of all genes of interest in a single test, which is now the mainstay for genetic diagnosis. Interpretation of data is challenging and requires expert knowledge in data handling, bioinformatics and clinical genetics.