We have previously developed bare narrow-bore capillary chromatography. In this work, high-performance DNA separation was realized for a size range of 10–800 base pairs(bp) utilizing bare narrow-bore capillary chromatography with 750 nm- radius capillaries. Separation behavior of double-stranded DNA(ds DNA) fragments was investigated over a range of eluent concentrations and elution pressures. DNA molecules were hydrodynamically separated in a size-dependent manner in free solution without any sieving matrices, with the longer fragments being eluted out from the capillary earlier. It was found that the eluent concentration variously influenced the transport behavior for different-sized DNA fragments depending upon the configuration of DNA molecules and the association of counterions. Ionic strength of the solutions strongly impacted DNA persistence length. Enhanced elution pressure could shorten analysis time with a slight loss in resolution. Excellent efficiency of two million theoretical plates per meter was achieved, which indicates the enormous potential of bare narrow-bore capillary chromatography for the analysis of DNA fragments. These findings would be useful in understanding the transport behavior of DNA fragments in confined dimensions for chromatography in free solution. In this work, high-performance DNA separation was realized for a size range of 10-800 base pairs (bp) utilizing bare narrow-bore capillary chromatography with 750 nm-radius capillaries. Separation behavior of double-stranded DNA (ds DNA) fragments was investigated over a range of eluent concentrations and elution pressures. DNA molecules were hydrodynamically separated in a size-dependent manner in free solution without any sieving matrices, with the longer fragments being eluted out from the capillary earlier. It was found that the eluent concentration variously influenced the transport behavior for different-sized DNA fragments depending upon the configuration of DNA molecules and the association of counterions. Ionic strength of the solutions strongly impacted DNA persistence length. Enhanced elution pressure could shorten analysis time with a slight loss in resolution. Excellent efficiency of two million theor etical plates per meter was achieved, which indicates the enormous potential of bare narrow-bore capillary chromatography for the analysis of DNA fragments. These findings would be useful in understanding the transport behavior of DNA fragments in confined dimensions for chromatography in free solution.