1. A method for determining the risk of aneuploidy of at least one chromosome or chromosome segment of interest in the genome of a fetus, the method comprising: performing a multiplex amplification to amplify at least 100 non-polymorphic loci per chromosome targeted and at least 100 SNP loci of free floating maternal and fetal DNA in a maternal blood, plasma, or serum sample using a plurality of probes to obtain amplified products; performing microarray analysis to measure the genetic data at a plurality of amplified SNP loci on at least one chromosome that is expected to be disomic in both the mother of the fetus and the fetus; performing microarray analysis to measure the genetic data at a plurality of amplified non-polymorphic loci; creating one or more hypotheses specifying the number of copies of the at least one chromosome or chromosome segment of interest in the genome of the fetus; determining the probability of each of the hypotheses of the number of copies of the at least one chromosome or chromosome segment of interest using the measured genetic data from the plurality of amplified SNP loci and the measured genetic data from the plurality of amplified non-polymorphic loci; and determining the risk of aneuploidy of the at least one chromosome or chromosome segment of interest using the determined probabilities of each of the hypotheses.