Background A baby in neonatal intensive care with respiratory insufficiency, skeletal dysplasia and dysmorphism was clinically suspected to have paternal uniparental disomy of chromosome 14 (UPD14). Molecular testing for UPD14 was requested. Methods Microsatellite markers on chromosome 14 were geno-typed in the affected child and both parents. Standard karyotype and interphase FISH using probes that map to 14qter were performed on the proband. SNP microarray (Illumina HumanCytoS-NP-12) was performed on the parent-child trio. Results Single nucleotide polymorphism (SNP) microarray detected a copy number neutral segment showing loss of heterozy-gosity (LOH) of approximately 12 Mb in size at the 14q terminus in the proband, encompassing the UPD14 critical imprinted region at 14q32. A SNP trio analysis showed that this segment was of paternal origin only in the proband, while the remainder of chromosome 14 showed biparental inheritance. The results of microsatel-lite and cytogenetic analyses were consistent with SNP microarray results. Conclusions A diagnosis of segmental paternal isoUPD14 was confirmed, consistent with the clinical presentation. SNP micro-array fully characterised the molecular abnormality in this case and may be an efficient replacement for traditional microsatellite-based UPD analyses.