A method of determining at least a portion of the genome of an unborn fetus of a pregnant female, the fetus having a father and a mother being the pregnant female, and the father having a paternal genome with paternal haplotypes and the mother having a maternal genome with maternal haplotypes, the method comprising: (a) analyzing a plurality of nucleic acid molecules from a biological sample obtained from the pregnant female, where the biological sample contains a mixture of maternal and fetal nucleic acids and wherein analyzing a nucleic acid molecule includes: (i) identifying a location of the nucleic acid molecule in the human genome; and (ii) determining a respective allele of the nucleic acid molecule; (b) determining a paternal allele inherited by the fetus from the father at each of a first plurality of loci, the identified locations of the nucleic acids of the biological sample determined in (a)(i) including the first plurality of loci, wherein the first plurality of loci are on a same chromosome, wherein the maternal genome is heterozygous at the first plurality of loci; (c) determining each of two maternal haplotypes of the first plurality of loci; (d) based on the determined alleles of the nucleic acid molecules at the first plurality of loci, a computer system determining amounts of respective alleles at each of the first plurality of loci; (e) comparing relative amounts of the respective alleles of the nucleic acid molecules at more than one locus of the first plurality of loci; and (f) based on the comparison, determining which of the two maternal haplotypes is inherited by the unborn fetus from the mother at the portion of the genome covered by the first plurality of loci. (a) analyzing a plurality of nucleic acid molecules from a biological sample obtained from the pregnant female, where the biological sample contains a mixture of maternal and fetal nucleic acids and wherein analyzing a nucleic acid molecule includes: (i) identifying a location of the nucleic acid molecule in the human genome; and (ii) determining a respective allele of the nucleic acid molecule; (i) identifying a location of the nucleic acid molecule in the human genome; and (ii) determining a respective allele of the nucleic acid molecule; (b) determining a paternal allele inherited by the fetus from the father at each of a first plurality of loci, the identified locations of the nucleic acids of the biological sample determined in (a)(i) including the first plurality of loci, wherein the first plurality of loci are on a same chromosome, wherein the maternal genome is heterozygous at the first plurality of loci; (c) determining each of two maternal haplotypes of the first plurality of loci; (d) based on the determined alleles of the nucleic acid molecules at the first plurality of loci, a computer system determining amounts of respective alleles at each of the first plurality of loci; (e) comparing relative amounts of the respective alleles of the nucleic acid molecules at more than one locus of the first plurality of loci; and (f) based on the comparison, determining which of the two maternal haplotypes is inherited by the unborn fetus from the mother at the portion of the genome covered by the first plurality of loci.