Allelic level matching is critical in bone marrow transplantation. Numerous reports provided evidences that superior graft outcome and graft versus host disease free status are related to allelic (high resolution typing) level of matching at HLA-A, B, Cw, DR and DQ loci. Sequence based typing (SBT) technology appeared to be the most sophisticated and accurate. Visible Genetics automated sequencer is currently used at our transplant center HLA laboratory. Sophisticated software permits allele assignments at HLA-A, B, Cw and DR loci. Here we present cases of ambiguous results of HLA-DR and Cw typing obtained by SBT method. In the first case, the DRB1 template to be analyzed spanned 225 bp, covering 98% of polymorphic regions located at 2^nd exon. The amplicon sequence was generated by amalgamation of 5’ and 3’ directions. We obtained the following three different allele combinations having the same alignment score and similarity to the reference sequence: DRB1*1104/1301; DRB1*1103/1306; DRB1*1116/1311. The detailed sequence analysis of these allele combinations revealed that ambiguities were located at 99 (T/C), 102 (A/G), 109 (A/T), 173 (A/C), 174 (G/C), 199 (A/T), 211 (A/G) and 212 (G/A) polymorphic regions, making further analysis impossible. To address this problem we used the One Lambda DR11/DR13 PCR-SSP high-resolution subtyping kit, which allowed us to determine the DRB1*1104/1301 genotype of the sample. Sequence comparison analysis confirmed the location of mismatched bases at positions predicted by SBT method. These data demonstrate that DR11/DR13 heterozygous samples present allele combinations requiring additional tests to obtain allelic level of typing, the PCR-SSP high resolution subtyping kit being suitable for this. A second case of ambiguous SBT results was observed for an acute myelogenous leukemia patient sample. HLA-A, B and DR typing clearly revealed genotypes at these loci. However, HLA-Cw SBT demonstrated Cw*0701/0706 association without any ambiguities located in the 2^nd or 3^d exons. Detailed analysis of DNA sequences of the entire genes, using Gene Bank database, revealed that these alleles differ only by two bases located at 902 (A/T) base (5^th exon – transmembrane region) and 1043 (C/T) base (6^th exon – cytoplasmatic region). The protein products of these genes are not expressed on the cell surface and do not play any role from immunological or clinical points of view. To obtain unambiguous high resolution typing results, two 5’ primers specific for Cw*0701 and Cw*0706 alleles were designed. Typing results revealed the presence of Cw*0701 allele. Family studies and direct sequencing of PCR product confirmed sample homozygocity at the Cw locus. In summary, our data demonstrate that SBT methodology does not always provide the allelic level of HLA typing. To obtain the proper allele assignment, combination of other high resolution typing techniques with confirmatory sequence analysis using the Gene Bank database is required.