Introduction: Next-generation sequencing (NGS) has transformed the diagnosis of rare paediatric disorders with heterogeneous and overlapping phenotypes. We evaluated the diagnostic yield and clinical utility of genome-scale sequencing across a broad spectrum of paediatric indications. Case presentation: We analysed 100 singleton NGS tests performed in children aged 1 day to 18 years (53 males, 47 females). Testing included 90 whole-exome sequencing (WES), 5 wholegenome sequencing (WGS), and 5 blended genome–exome sequencing (BGE). Actionable pathogenic/likely pathogenic (P/LP) variants were identified in 84% of cases. A phenotyperelated molecular diagnosis was established in 63%, while 22% had incidental or carrier-only findings; 16% were negative. Among phenotype-positive cases, zygosity included heterozygous (n=31), homozygous (n=21), hemizygous (n=4), and compound heterozygous variants (n=7), with trans phase confirmed in 6 cases through orthogonal testing or bioinformatic phasing. Inheritance patterns were predominantly autosomal dominant (n=31) and autosomal recessive (n=28), with fewer Xlinked cases. Missense variants were the most frequent (54.3%), followed by nonsense (20.0%) and splice-site variants (11.4%), with frameshift, indel, and CNV events collectively accounting for 14.3%. The highest diagnostic yield was observed in neurodevelopmental and epileptic disorders (23/34), followed by metabolic/ endocrine (11/17) and neuromuscular/peripheral nervous system disorders (9/12). WGS achieved a 100% diagnostic yield, including the identification of a clinically relevant CNV missed on WES. Conclusions: Genome-scale sequencing demonstrates a high diagnostic yield and substantial clinical impact in paediatric rare diseases, ending diagnostic odysseys, enabling targeted management, and supporting family counselling. Strategic use of WGS complements WES, particularly in unresolved cases.