We present an experimental study of the microfluidic electrophoresis of long DNA in self-assembling matrixes of magnetic bead columns. Results are presented for the rapid separation of λ-phage, 2λ-DNA, and bacteriophage T4 DNA, where separation resolutions greater than 2 between λ and T4 are achieved in times as short as 150 s. The use of a computer-piloted flow control system and injection results in high reproducibility between separations. We compare the experimentally measured mobility and dispersion with an exactly solvable lattice Monte Carlo model. The theory predicts that the mean velocity scales linearly with the field, the band broadening scales with the inverse of the field, and the resolution is independent of the field for intermediate fields-all of which are in accord with the experimental results. Moreover, reasonable quantitative agreement is achieved for band broadening for longer DNA (2λ and T4) when the average postengagement time is measured experimentally. This work demonstrates the possibility of achieving fast microfluidic separation of large DNA on a routine basis.