A method of determining a fetal DNA percentage in a biological sample from a pregnant female with at least two fetuses, the biological sample comprising fetal and maternal DNA, the method comprising: creating a histogram by: for each of a plurality of chromosomal regions: identifying one or more loci in the respective chromosomal region at which a respective first allele and a respective second allele are detected in the biological sample; measuring, at the one or more loci, a first amount of the one or more first alleles and/or a second amount of the one or more second alleles in the biological sample; obtaining a normalized parameter for the first amount or the second amount; and incrementing counters based on a number of chromosomal regions with specified values for the normalized parameter; fitting a linear combination of probability distributions to the histogram, where the fetal DNA percentage is an input to the linear combination of probability distributions; and varying the input fetal DNA percentage to find an optimal fetal DNA percentage that optimizes a fit of the linear combination of probability distributions to the histogram. creating a histogram by: for each of a plurality of chromosomal regions: identifying one or more loci in the respective chromosomal region at which a respective first allele and a respective second allele are detected in the biological sample; measuring, at the one or more loci, a first amount of the one or more first alleles and/or a second amount of the one or more second alleles in the biological sample; obtaining a normalized parameter for the first amount or the second amount; and incrementing counters based on a number of chromosomal regions with specified values for the normalized parameter; fitting a linear combination of probability distributions to the histogram, where the fetal DNA percentage is an input to the linear combination of probability distributions; and varying the input fetal DNA percentage to find an optimal fetal DNA percentage that optimizes a fit of the linear combination of probability distributions to the histogram. for each of a plurality of chromosomal regions: identifying one or more loci in the respective chromosomal region at which a respective first allele and a respective second allele are detected in the biological sample; measuring, at the one or more loci, a first amount of the one or more first alleles and/or a second amount of the one or more second alleles in the biological sample; obtaining a normalized parameter for the first amount or the second amount; and incrementing counters based on a number of chromosomal regions with specified values for the normalized parameter; identifying one or more loci in the respective chromosomal region at which a respective first allele and a respective second allele are detected in the biological sample; measuring, at the one or more loci, a first amount of the one or more first alleles and/or a second amount of the one or more second alleles in the biological sample; obtaining a normalized parameter for the first amount or the second amount; and incrementing counters based on a number of chromosomal regions with specified values for the normalized parameter; fitting a linear combination of probability distributions to the histogram, where the fetal DNA percentage is an input to the linear combination of probability distributions; and varying the input fetal DNA percentage to find an optimal fetal DNA percentage that optimizes a fit of the linear combination of probability distributions to the histogram.