Abstract Background: The single nucleotide polymorphism (SNP) microarray technology has emerged as a powerful tool to screen the whole genome for sub-microscopic duplications and deletions that are not detectable by traditional cytogenetic analysis. Case: We report a case of a female twin born at 27^th week of gestation who died 1 day after birth whereas the co-twin survived without complications. The case twin was referred to our unit for autopsy, and in addition we performed an SNP microarray analysis. Results: Three copy number variants (CNVs) were identified by the SNP microarray analysis. The most interesting CNV in relation to the clinical phenotype (pulmonary immaturity) was a disruption in the gene ST6GALNAC3 (1p31.1) that is involved in the biosynthesis of gangliosides. Conclusions: It is unknown from this case report whether the CNV at 1p31.1 contributes to a genetic predisposition that is related to maturation of the lungs or the perinatal death of one of the twins. However, disruptions in the biosynthesis of gangliosides have been previously associated with premature death in mice.