We report on the prenatal diagnosis, genetic studies, and pathology of a case with de novo isochromosome 13q. A 31-year-old primigravida was referred for genetic counselling at 26 weeks' gestation due to the sonographic findings of intrauterine growth retardation and microcephaly. Level II ultrasonograms further demonstrated alobar holoprosencephaly, hypotelorism, polydactyly, a ventricular septal defect, and a single nostril. A diagnosis of cebocephaly was made. Genetic amniocentesis and cord blood sampling revealed translocation trisomy 13 with a de novo t(13q13q) rearrangement. Chromosomal analysis using G- and C-banding techniques and fluorescence in situ hybridization (FISH) showed an apparent monocentric isochromosome. Molecular analyses using polymorphic molecular markers showed that the rearrangement was consistent with an isochromosome of maternal chromosome 13q[46,XX,i(13)(q10)]. Necropsy confirmed cebocephaly and the prenatally detected anomalies.