Background: Schimke immunoosseous dysplasia (SIOD) is a rare autosomal recessive multisystem disorder due to biallelic variants in SMARCAL۱, characterized by growth failure, skeletal dysplasia, immunodeficiency, and renal involvement. In populations with consanguineous marriages, genomic evaluation plays a pivotal role in diagnosing multisystem pediatric conditions that may elude conventional testing. Methods: A ۴-year-old Iranian boy from a consanguineous family was referred for genetic evaluation. His prenatal course was notable for intrauterine growth restriction (IUGR) secondary to poor placental perfusion; he was born at ۳۴ weeks and required a ۳۵-day neonatal admission for jaundice. Clinical features included visual impairment and craniofacial dysmorphism (low-set ears, micrognathia, prominent forehead, upturned eyelashes). Conventional cytogenetic analysis repeatedly failed due to absence of metaphase cells, and chromosomal breakage testing was reported as normal. Whole exome sequencing (WES) was subsequently performed. Results: WES identified a homozygous missense variant in SMARCAL۱ (NM_۰۱۴۱۴۰.۴:c.۱۶۸۲GA, p.(Arg۵۶۱His)), classified as likely pathogenic and consistent with autosomal recessive SIOD. Following the molecular diagnosis, immunologic evaluation revealed lymphocyte deficiency, providing a plausible explanation for the inability to obtain metaphases in standard karyotype cultures. Conclusion: This case illustrates how SIOD can present with neonatal complications, dysmorphic features, and immunodeficiency that interfere with routine cytogenetic assays. Genomic testing (WES) was decisive in establishing the diagnosis. The report underscores the necessity of early comprehensive genetic evaluation in complex pediatric cases-particularly in consanguineous populations-where conventional laboratory methods may be inconclusive. Further functional studies and broader case series are needed to expand understanding of genotype-phenotype correlations in SIOD.