Pathogenic variants in voltage-gated sodium channels (VGSC) may cause disturbed sensory function, including small fiber neuropathy (SFN) in adults, but little is known about their role in children and adolescents. 39 prospectively enrolled children (age 12.03 ± 4.61 years) with abnormal pain sensation underwent detailed diagnostics including quantitative sensory testing (QST, if > 5 years old), quality of life assessment and genetic studies for VGSC variants and further etiologies. QST results complied with Aẟ- und C-fiber damage, including increased cold, warmth and mechanical detection thresholds, higher thermal sensory limen and allodynia. Intraepidermal nerve fiber densities were low in 7 / 17 children. This resulted in a great impact on physical quality of life and pain scales but not on social life. Five children showed heterozygous variants of unknown significance (VUS) in genes encoding VGSC (SCN9A, n=2; SCN10A, n=3) with maternal or paternal inheritance in two and one patient, respectively. Three further patients showed likely disease-associated variants in the HUWE1, TRIO and PYGM genes. Despite a high disease burden and small fiber damage indicated by QST and skin histology, only VUS in VGSC and additional monogenic causes of pain symptoms outside of VGSC genes were identified. Genetic studies in affected children should therefore be comprehensive, not restricted to VGSC variants and be supplemented by a detailed clinical workup. In silico modelling and future functional studies might help to identify VUS that play a role in altered pain perception.