A method for molecular haplotyping of a subject is disclosed. The method comprises: randomly selecting a set of chromosomes in each of a plurality of lyzed diploid cells of the subject, collecting the selected chromosomes from said plurality of cells into a plurality of sample tubes, wherein each sample tube contains chromosomes selected from one or more cells, genotyping genomic DNA in each sample tube, and determining haplotype of the alleles based on allele nucleotide sequence information and corresponding nucleotide signal intensities from genotyping data. Other methods for molecular haplotyping using single cell lysate or single cell microdissection are also disclosed.