Down syndrome (DS) is the most common chromosomal abnormality and is associated with an extra copy of the chromosome 21. Although several markers are commonly used during pregnancy for the screening of DS, the definitive diagnosis is based on karyotype after amniocentesis, which is an expensive and laborious analysis. S100B is an astrocyte protein which had its gene mapped to the long arm of chromosome 21. Previous preliminary reports have found increased levels of this protein in the amniotic fluid of DS gestations. Aiming to achieve a simpler and cheaper test then karyotype to perform prenatal diagnosis of DS, here we have extended our previous studies and evaluated the real usefulness of amniotic S100B measurement for prenatal DS diagnosis. We have measured S100B in amniotic fluid of 96 pregnancies with DS and of 50 normal pregnancies. Pregnancies with DS presented significantly higher amniotic fluid S100B levels (M = 1.16 ng/mL; IQ = 0.83/1.78) than normal pregnancies (M = 0.51 ng/mL; IQ = 0.38/0.83) (p < 0.0001). A receiver operating characteristic (ROC) curve was performed to evaluate the sensitivity and specificity of S100B for DS diagnosis, and presented an area under the curve (AUC) of 0.82, indicating that S100B could be a reliable marker of DS. Moreover, values above 1.67 ng/mL were present only in DS fetuses, representing about 30% of affected pregnancies. However, as an overlap of values was observed between normal and DS gestations, we concluded that amniotic S100B alone is not a good test to discard DS diagnosis.