Trichohepatoenteric syndrome (THES) is a rare autosomal, recessively inherited disorder. Mutations in the tetratricopeptide repeat domain 37 (TTC37) gene and the superkiller viralicidic activity 2‑like (SKIV2L) gene have been identified to cause THES. The present study reported a case of a Chinese boy, who presented clinically with intrauterine growth retardation, intractable diarrhea, facial dysmorphism, abnormal scalp hair shafts, immune disorders and liver involvement. Targeted next‑generation sequencing and Sanger DNA sequencing showed compound heterozygous mutations of the SKIV2L gene. The present study was the first, to the best of our knowledge, to report a case of a boy with THES resulting from compound heterozygous mutations of the SKIV2L gene in China. Target sequence capture combined with high‑throughput next‑generation sequencing technologies have shown to be effective methods for the molecular genetic assessment of rare inherited disorders.