Partial duplications and deletions of chromosome 13 are rare and the phenotypic expressions of both aneuploidies are highly variable. Here we report on a fetus diagnosed prenatally with partial trisomy of 13q and a diaphragmatic hernia as a sole malformation. The parents had decided to terminate the pregnancy after the finding of diaphragmatic hernia by ultrasound scan, which was also confirmed by autopsy of the fetus. Subsequently chromosome analysis, fluorescence in situ hybridization (FISH), and array comparative genomic hybridization (array CGH) was carried out on fetal tissue. The chromosome analysis revealed additional material on chromosome 13, which was shown to be from the same chromosome, by FISH analysis. Array CGH demonstrated a partial duplication and a small deletion at the distal long arm of chromosome 13. The parents had normal karyotypes. This is the first case of a de novo pure partial duplication of 13q31.3-q34 and distal deletion of 13q34 with a phenotype apparently only involving a diaphragmatic hernia and three lung lobes on both sides. Microarray analysis was useful in refining the chromosomal imbalance and suggesting a candidate region for diaphragmatic hernia.