A microfluidic counter current dialysis device for size based purification of DNA is described. The device consists of two polydimethylsiloxane (PDMS) channels separated by a track etched polycarbonate membrane with a 50 nm pore size. Recovery of fluorescein across the membrane was compared with 10 and 80 nucleotide (nt) ssDNA to characterize the device. Recovery of all three analytes improved with decreasing flow rate. Size selectivity was observed. Greater than 2-fold selectivity between 10 nt and 80 nt ssDNA was observed at linear velocities less than 3mm s-1. Increasing the ionic strength of the buffer increased transport across the membrane. Recovery of 80 nt ssDNA increased over 4-fold by adding 30mM NaCl to the buffer. The effect was size dependent as 10 nt showed a smaller increase while the recovery of fluorescein was largely unaffected by increasing the ionic strength of the buffer.