The immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is a rare autosomal recessive disorder characterized by variable immunodeficiency, instability of the pericentromeric heterochromatin, and facial dysmorphism. Here we report a new case of ICF syndrome who died of rubella pneumonitis. A six year-old-girl who was the first child of consanguineous parents was admitted to the hospital because of bronchopneumonia. Laboratory investigations revealed pan-hypogammaglobulinemia, lymphoperria, normal proportions of peripheral blood lymphocytes with an inverted CD4/CD8 ratio, and interstitial pneumonia with a positive serology of acute rubella infection. The ICF syndrome was diagnosed by centromeric instability in the standard cytogenetic analysis. An inclusion body was demonstrated in the lung biopsy after the death of the patient. Chromosomal investigation could be helpful along with other tests for diagnosis of variable immunodeficiency accompanied by facial dysmorphism.