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: measuring genetic data at a plurality of loci on at least one chromosome that is expected to be disomic in both the mother of the fetus and the fetus, in a maternal blood, plasma, or serum sample comprising free floating maternal and fetal DNA; determining a ratio of fetal to maternal DNA in the blood, plasma, or serum sample using the measured genetic data at the plurality of loci on the at least one chromosome that is expected to be disomic; measuring genetic data at a plurality of loci on at least one chromosome or chromosome segment of interest in the sample; 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, on a computer, 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 at least one chromosome or chromosome segment of interest and the ratio of fetal to maternal DNA; and determining, on a computer, the risk of aneuploidy of the at least one chromosome or chromosome segment of interest using the determined probabilities of each of the hypotheses.