Human DNA quantification is an important step for subsequent short tandem repeat (STR) analysis and interpretation because it can provide various information on the quantity and quality for the extracted DNA. In this study, we compared four commercially available quantification kits based on a TaqMan assay and an intercalating-dye based quantification kit. The following three points were investigated: 1) variations of the average peak heights among individuals when 1 ng of DNA, the amount being determined by each quantification kit, was amplified using GlobalFiler and Yfiler Plus PCR Amplification Kits, 2) effect of the presence of a female DNA on the quantification of male DNA, and 3) relationship between “Degradation Index” and the STR electropherograms. The average peak heights generated using GlobalFiler showed less individual-dependent variations in the four TaqMan based kits than the intercalating-dye based kit. The average peak heights generated using Yfiler Plus showed similar variations among the three TaqMan based kits capable of male DNA quantification along with total human DNA. The presence of a large amount of female DNA had little effect on male DNA quantification in all the three kits. When highly degraded DNA samples were quantified, the “Degradation Indices” differed significantly among three kits. It was probably due to the different amplicon sizes of the long fragment targets among kits. Before implementing a new human DNA quantification kit in casework, it is essential to understand the characteristics of the adopted quantification kit.