Despite the NGS revolution, the diagnostic yield of many inherited disorders remains unsatisfactory. One key example is Joubert syndrome (JS), a recessive ciliopathy for which >40 genes are known. After panel sequencing or WES, up to 30-35% patients (in our cohort 172/475) fail to receive a definite diagnosis, hampering counselling, management and prenatal testing. We hypothesized that a relevant proportion of these cases are caused by cryptic variants within known genes, and that at least a subset can be diagnosed by reanalyzing available NGS data, as sequences partly cover introns, although at a much lower coverage. To prove this, we focused on 35 JS patients in whom only a single coding pathogenic variant in a known JS gene had been found. We first reanalyzed NGS data searching for CNVs, and identified 6 distinct intragenic heterozygous deletions in 8 cases. CNVs were confirmed by RT-PCR and were in trans with the exonic variant. Next, we searched for rare intronic variants bioinformatically predicted to impact splicing and identified 10 candidate variants (one recurring in 3 cases), placed up to 200bp from exon boundaries, all in trans with the exonic variant. So far, we tested 7 variants (from 9 patients) by RT-PCR on patients' cDNA and/or in vitro minigene assays. Notably, all variants were shown to induce overt splicing defects, resulting either in frameshift, in frame deletions or insertions. One of these variants was also found in homozygosity in another JS negative case. Minigene assays of the remaining 3 variants are in progress, while we are now performing RNAseq in patients lacking candidate intronic variants detectable by WES. In conclusion, WES reanalysis focused on CNVs and intronic variants allowed detecting the "second hit" in >50% patients carrying heterozygous coding variants. We provide proof of principle that cryptic variants are common mutational events in JS, and their search results in a significant increase of the diagnostic yield.