Salla disease (SD) is an autosomal recessive disorder in which free sialic acid (N-acetyl neuraminic acid) accumulates in lysosomes. A specific transport mechanism for acidic monosaccharides on the lysosomal membrane has recently been described, but the molecular deficiency causing SD is still unknown. We have previously mapped the SD gene to 6q14-q15 by means of genetic linkage analysis and restricted the positive chromosomal area to less than 100 kb with linkage disequilibrium mapping. The two best allelic association markers have now retrospectively been used in five prenatal analyses originally studied with sialic acid assays in chorionic villus specimens. In four cases an unaffected fetus was predicted with a probability level of more than 94%, which was in concordance with the biochemical data. One fetus was predicted to be affected with over 96% probability, as was shown by free sialic acid assays in a CVS sample and in fetal tissues after termination of the pregnancy. Risk calculations incorporating disequilibrium were also used to predict the carrier status in members of six families with previous SD cases, and also in a few cases with no known family history of SD. DNA marker based analysis thus provides a reliable method for risk estimations in prenatal cases and for carrier identification of SD.