Next generation sequencing has enabled a broad and growing knowledge on total genomes and transcriptomes.Many new methods have been developed in biology and more and more results are entering medical sciences.However, after more than 4 years, reports are showing new applications for medical diagnostics, where conventional sequencing might not be sufficient enough.Ultra deep sequencing for HIV resistance, HIV genotyping and multiple applications in oncology seem to provide more information on viral or cell clones which might develop in later disease.Sequencing has here the purpose to predict the right therapeutic option.Additionally, some reports show, that fundamental problems in HLA testing might be overcome by next generation sequencing.Hematopoietic stem cell transplantation requires high resolution HLA-typing to prevent a very high morbidity and mortality of patients.All methods are directed to find the best match of donor/recipient pairs, because a mismatch increases the risk for severe acute graft versus host disease and transplant dysfunction.However, time to transplantation is also an important factor for patient survival.This leads to the problem that a meticulously applied diagnostic method has to be performed under restraint.Conventional Sanger sequencing is still the gold standard in HLA-genotyping.To avoid overload many laboratories restrict their typing to one or two exons and therefore are not able to resolve null-alleles or ambiguities in other exons.Moreover, unclear phasing are a greater problem to generate clearly distinguishable results.Heterozygous samples lead to the most common ambiguities and require additional genotyping of family members.Up to 41% of HLA-A and 24% of HLA-B are ambiguous in genotyping.Additional genotyping results in a longer waiting time for the patient and therefore adds risks.This strategy may not be applicable for donors and donor registries or cord blood banks.