We describe the first case of mosaic supernumerary marker iso (8p) displaying a karyotype discordance between chorionic villi (CV) and amniotic fluid (AF) cultures during prenatal cytogenetic diagnosis. In the first trimester, cytogenetic analysis after chorionic villi sampling (CVS) was normal in all metaphases in the short-term cytotrophoblast cell culture, but an undefined supernumerary marker was detected in 60% of mesenchymal cells in the long-term CV culture. Informed of the mosaicism, the couple selected amniotic fluid sampling as a second-trimester confirmatory diagnostic procedure. The supernumerary marker was absent in all of the 25 available AF cells metaphases. The prospective parents received genetic counselling and were informed that the discordance could be interpreted as a placental confined mosaicism or as a true foetal mosaicism with low percentage of affected cells. The couple opted to continue the pregnancy. In the second month of life, the child had abnormal development with severe psychomotor delay and frequent episodes of epilepsy. Postnatal cytogenetic extensive re-evaluation discovered that the previously detected supernumerary marker was indeed an isochromosome (8p) rearrangement present at low frequency in 5% of the blood lymphocytes.