Autosomal Dominant Polycistic Kidney Disease (ADPKD) is the most common inherited genetic disorder in the word, caused by mutations in PKD1 gene in 85% of cases and PKD 2 gene in the remaining 15%. Although diagnosis is usually based on ultrasound, MRI and CT scans, in some cases genetic testing is necessary, for example, in patients with atypical phenotype or with a negative family history, or in cases of donation from relatives. The presence of pseudogenes in PKD1, the size of the gene, the costs of the Sanger sequencing and genetic heterogeneity underlying kidney disease make genetic analysis particularly difficult to be performed. Next Generation Sequencing (NGS) represents the last frontier of innovation among diagnostic tools for molecular diagnosis of inherited cystic kidney disease thanks to the ability to analyze several genes at the same time. In this regard, we have developed a NGS platform, called Nephroplex, with the aim of identifying variations in 115 genes responsible for numerous kidney diseases, including cystic and polycystic disease, achieving, overall, a target region of 338.8 kbps. The technology used for the enrichment is HaloPlex system, based on the digestion of genomic DNA with restriction enzymes and the capture of the regions of interest with specific hybridization probes. With our platform, we have analyzed 9 patients with clinical diagnosis of ADPKD. We have obtained a depth coverage of 100x for 96.5% of the target, while the region not covered accounted for only 3% of the region of interest. In 6 patients, we found causative mutations in the genes PKD1 and PKD2, achieving a detection rate of 66%. In conclusion, the NephroPlex platform has proved to be an excellent device for molecular diagnosis of kidney disease and could clarify the mechanisms underlying genetic heterogeneity observed in kidney disease.