A method for determining fetal aneuploidy of chromosome of interest from a maternal blood sample comprising a mixture of cell-free DNA molecules of fetal and maternal origin, said method comprising: a) isolation of cell-free DNA from maternal blood; b) performing a random sequencing on at least a portion of a plurality of the cell-free DNA molecules contained in the blood, the portion comprising DNA corresponding to at least one chromosome of interest and a plurality of presumably euploid chromosomes, thereby obtaining plurality of sequence reads; c) mapping the sequence reads to the reference human genome, thereby obtaining plurality of mapped tags; d) splitting said reference human genome into 1Mbp subsequent and non-overlapping bins; e) determination of distribution of the tags to said bins and whole chromosomes according to their mapping location; f) determining fractional bin value FB as a ratio of number of tags mapped to the bins for chromosome of interest in the sample to the number of tags mapped to internal reference bins IRB; g) determining sample multinomial mean μ ( n) and multinomial standard deviation σ (n); wherein μ ( n) and σ (n) are calculated for a random variable defined as a ratio between number of tags mapped to the chromosome of interest in the sample and the sum of tags mapped to internal reference bins IRB, wherein the probability distribution of mapping of the tags to the chromosome of interest and to the internal reference bins IRB is multinomial, and the parameters of said multinomial distribution are determined from the training set of euploid blood samples; h) determining z-score value as a difference between fractional bin value FB and multinomial mean μ ( n) divided by multinomial standard deviation σ (n); and i) comparing z-score value to at least one cut-off value to determine whether an aneuploidy exists for the chromosome of interest; wherein, as a prerequisite of the steps f)-i), a training set of euploid blood samples is subjected to essentially the same procedures consisting of steps a)-e) above and then the following steps are performed: f') choosing internal reference autosomes IRA from candidate internal reference autosomes on the basis of the coefficient of variation CV thereof, while potentially aneuploid chromosomes are excluded; g') choosing the internal reference bins IRB by an genetic algorithm from two candidate sets, the first candidate set being set of randomly selected bins, while bins corresponding to potentially aneuploid chromosomes are excluded, and the second candidate set being the set of bins corresponding to the best internal reference autosomes IRA determined in the previous step f'. a) isolation of cell-free DNA from maternal blood; b) performing a random sequencing on at least a portion of a plurality of the cell-free DNA molecules contained in the blood, the portion comprising DNA corresponding to at least one chromosome of interest and a plurality of presumably euploid chromosomes, thereby obtaining plurality of sequence reads; c) mapping the sequence reads to the reference human genome, thereby obtaining plurality of mapped tags; d) splitting said reference human genome into 1Mbp subsequent and non-overlapping bins; e) determination of distribution of the tags to said bins and whole chromosomes according to their mapping location; f) determining fractional bin value FB as a ratio of number of tags mapped to the bins for chromosome of interest in the sample to the number of tags mapped to internal reference bins IRB; g) determining sample multinomial mean μ ( n) and multinomial standard deviation σ (n); wherein μ ( n) and σ (n) are calculated for a random variable defined as a ratio between number of tags mapped to the chromosome of interest in the sample and the sum of tags mapped to internal reference bins IRB, wherein the probability distribution of mapping of the tags to the chromosome of interest and to the internal reference bins IRB is multinomial, and the parameters of said multinomial distribution are determined from the training set of euploid blood samples; h) determining z-score value as a difference between fractional bin value FB and multinomial mean μ ( n) divided by multinomial standard deviation σ (n); and i) comparing z-score value to at least one cut-off value to determine whether an aneuploidy exists for the chromosome of interest; f') choosing internal reference autosomes IRA from candidate internal reference autosomes on the basis of the coefficient of variation CV thereof, while potentially aneuploid chromosomes are excluded; g') choosing the internal reference bins IRB by an genetic algorithm from two candidate sets, the first candidate set being set of randomly selected bins, while bins corresponding to potentially aneuploid chromosomes are excluded, and the second candidate set being the set of bins corresponding to the best internal reference autosomes IRA determined in the previous step f'.