DNA quantification is a routine yet important procedure that determines the efficacy of long-term sample storage and further manipulations with the sample. There are a few well-established methods for measuring DNA concentrations. However, it still not fully clear how concordant their results are. The aim of this work was to measure DNA concentrations in a set of samples using different quantification methods and to compare the obtained values. In 2 independent experiments, a total of 100 genomic DNA samples were analyzed using 3 different DNA quantification methods, including spectrophotometry (NanoDrop), fluorometry (Qubit) and real-time PCR (Quantifiler). The obtained relative concentrations demonstrated an excellent correlation (the correlation coefficients were as high as 0.98 to 0.99). However, the absolute concentrations showed a considerable variation and even a twofold difference. Spectrophotometry yielded the highest concentrations, whereas fluorometry yielded the lowest. The real-time PCR results were intermediate. The differences were more pronounced for the samples with low DNA concentrations. We recommend that such differences should be accounted for when estimating DNA concentrations using an arsenal of different quantification methods.