Gitelman's syndrome (GS) is a rare recessive disorder caused by mutations in the renal salt-handling genes SLC12A3 and CLCNKB. Our aim was to develop a next-generation sequencing (NGS) procedure for these genes based on two-tubes multiplex amplification of DNA pools and semiconductor sequencing with the Ion Torrent Personal Genome Machine (PGM). We created one pool with DNA from 20 GS patients previously Sanger sequenced for the coding exons of SLC12A3. A total of 13 mutations present in 11 of these patients were used as control variants to validate the NGS procedure. The full coding sequence of SLC12A3, CLCNKB and CLCNKA was amplified in only two Ampliseq tubes and processed and sequenced with the PGM. Large SLC12A3 and CLCNKB deletions were ascertained through multiplex ligation-dependent probe amplification in some patients. With the exception of the SLC12A3 exon 9, all the amplicons were successfully read and 12 of the 13 control variants were detected. The analysis of CLCNKB showed four putative mutations in the GS pool that were further assigned to specific patients. Two patients were heterozygous compounds for a single-nucleotide mutation and a large deletion at SLC12A3 or CLCNKB. We reported a NGS procedure that would facilitate the rapid and cost-effective large-scale screening of the three renal salt-handling genes. In addition to characterize the mutational spectrum of GS patients, the described procedure would facilitate the rapid and cost-effective screening of these genes at a population scale.