Single allele HLA disparity can sometimes be a result of a haplotype phase inversion and then both HLA haplotypes can be disparate. Haplotypic disparity is accompanied by the disparity of non-tested MHC components frequently remaining in linkage disequilibrium with known components. The aim of the study was to compare haplotype and HLA molecule disparities and their influence on the survival of hematopoietic stem cell transplanted (HSCT) patients. Transplanted in Polish centers in 2002-2012, N=587 donor-recipient pairs were stratified for the number of disparate HLA A-C-B-DRB1-DQB1 haplotypes (0, 1 or 2 disparate Hp) or the number of disparate HLA molecules (0, 1 or 2+3 disparate HLA). The most probable extended haplotype pairs were inferred using PHASE software. Kaplan-Meyer survival curves were plotted and one year overall survival (OS) of 3 groups were compared using Chi2 test, df.=2 and goodness of trend was compared between strata. When all N=587 donor-recipient pairs were stratified for the number of mismatched haplotypes (mmHp) or mismatched HLA molecules (mmHLA) their OS fit better to the number of mmHp than mmHLA (Chi2=7.64; p=0.022 and Chi2=6.39; p=0.041, respectively). The higher predictive power of mmHp than mmHLA was even more obvious when comparison was restricted to OS of N=457 patients presenting standard risk disease phase during transplantation (Chi2=7.86; p=0.019 and Chi2=6.34; p=0.042, respectively). The prediction of mmHp and mmHLA was not the case for N=97 patients presenting high risk disease phase during transplantation (Chi2=0.23; p=0.89 and Chi2=0.94; p=0.62, respectively). The number of disparate MHC haplotypes and HLA molecules are of vital importance for standard risk HSCT-recipients’ survival. The disparate MHC haplotypes are more harmful than disparate HLA molecules and should be equally considered during hematopoietic stem cell donor search/selection process. Supported by National Center of Science, project No. N N402 351138.