Aim To determine the level at which contaminating DNA will interfere with HLA typing by NexGen Sequencing. Methods Two separate DNAs were mixed 0.1–50%, and typed: rSSO (OneLambda®); NexGen (TruSight® HLA v2, Illumina®). Analysis: Fusion® and Conexio® Assign™, respectively. Results The table indicates at what percentage of contaminating DNA, interference occurs for detecting the correct HLA locus type. Except for DR, the results are similar. As little as 2% contamination may result in incorrect assignment of DRB1 by rSSO; NexGen is 10× lower. Overall, ∼20–80% contaminating DNA may allow for detection of all four alleles. Detection is much easier with rSSO, where the MFI values of the probes are easier to assess. Individual probe values near the cut-offs can be adjusted, and thereby reveal inappropriate type results, or the additional alleles may be seen as increasing heights of probe values not yet reaching the cutoffs. Detection may be more difficult with NexGen. Even when the control parameters are good, and read depths are >100, contaminating DNA can result in incorrect typing results. At least two noticeable issues contribute to incorrect results, even without contaminating DNA. (1) The alleles may asymmetrically amplify in the initial steps. Where one allele amplifies 10% or less of the two, the polymorphisms may fall into the “noise” range where they are not correctly identified by the software, even with good read depths. (2) The coverage across an allele may be poor in segments where important polymorphisms are missed. Contaminating DNA exacerbate these, so that a contaminating allele polymorphism may be assigned when the percentage of contamination is as noted in the Table. Conclusions Low levels of contaminating DNA can result in incorrect DRB1 assignment. Asymmetric amplification of alleles can exacerbate the effects of contaminating DNA, and may result in incorrect homozygosity assignment even without contaminating DNA. Careful awareness of linkage disequilibrium details can help to spot incorrect typing results.