A process to calculate a risk of fetal X or Y chromosomal aneuploidy in a maternal sample, wherein the determination, estimation and calculation steps are performed on a computer, the process comprising the steps of: interrogating one or more Y chromosomal loci in vitro; interrogating one or more X chromosomal loci in vitro; interrogating one or more polymorphic loci on at least a first autosome in vitro; calculating a fetal nucleic acid proportion in the maternal sample by analyzing a frequency of polymorphisms on the first autosome; determining whether the fetal nucleic acid proportion in the maternal sample is adequate to perform analysis estimating a relative I chromosome frequency for a Y chromosome and an X chromosome in the maternal sample in view of the fetal nucleic acid proportion; using the calculated fetal nucleic acid proportion, calculating values of likelihood that the fetal Y chromosome is present in no copies, one copy or two or more copies in the maternal sample; calculating a risk of aneuploidy of the fetal Y chromosome in the maternal sample by comparing the calculated values of likelihood to a first mathematic model assuming no copies of the Y chromosome, a second mathematic model assuming one copy of the Y chromosome and a third mathematic model assuming two or more copies of the Y chromosome; using the calculated fetal nucleic acid proportion, calculating values of likelihood that the fetal X chromosome is present in one copy, two copies or three or more copies in the maternal sample; and calculating a risk of aneuploidy of the fetal X chromosome in the maternal sample by comparing the calculated values of likelihood to a first mathematic model assuming one copy of the X chromosome, a second mathematic model assuming two copies of the X chromosome, and a third mathematic model assuming three or more copies of the X chromosome. interrogating one or more Y chromosomal loci in vitro; interrogating one or more X chromosomal loci in vitro; interrogating one or more polymorphic loci on at least a first autosome in vitro; calculating a fetal nucleic acid proportion in the maternal sample by analyzing a frequency of polymorphisms on the first autosome; determining whether the fetal nucleic acid proportion in the maternal sample is adequate to perform analysis estimating a relative I chromosome frequency for a Y chromosome and an X chromosome in the maternal sample in view of the fetal nucleic acid proportion; using the calculated fetal nucleic acid proportion, calculating values of likelihood that the fetal Y chromosome is present in no copies, one copy or two or more copies in the maternal sample; calculating a risk of aneuploidy of the fetal Y chromosome in the maternal sample by comparing the calculated values of likelihood to a first mathematic model assuming no copies of the Y chromosome, a second mathematic model assuming one copy of the Y chromosome and a third mathematic model assuming two or more copies of the Y chromosome; using the calculated fetal nucleic acid proportion, calculating values of likelihood that the fetal X chromosome is present in one copy, two copies or three or more copies in the maternal sample; and calculating a risk of aneuploidy of the fetal X chromosome in the maternal sample by comparing the calculated values of likelihood to a first mathematic model assuming one copy of the X chromosome, a second mathematic model assuming two copies of the X chromosome, and a third mathematic model assuming three or more copies of the X chromosome. <EOS>