We report the factors influencing the capture of DNA by DNA-modified microbeads confined within a microfluidic channel. Quantitative correlation of target capture efficiency to probe surface concentration, solution flow rate, and target concentration are discussed. The results indicate that the microfluidic system exhibits a limit of detection of similar to 10(-10) M (similar to 10(-16) mol) DNA and a selectivity factor of similar to 8 x 10(3). Typical hybridization times are on the order of minutes.