An effective method for in vivo chemical monitoring is to couple sampling probes, such as microdialysis, to online analytical methods. A limitation of this approach is that in vivo chemical dynamics may be distorted by flow and diffusion broadening during transfer from sampling probe to analytical system. Converting a homogeneous sample stream to segmented flow can prevent such broadening. We have developed a system for coupling segmented microdialysis flow with chip-based electrophoresis. In this system, the dialysis probe is integrated with a PDMS chip that merges dialysate with fluorogenic reagent and segments the flow into 8-10 nL plugs at 0.3-0.5 Hz separated by perfluorodecalin. The plugs flow to a glass chip where they are extracted to an aqueous stream and analyzed by electrophoresis with fluorescence detection. The novel extraction system connects the segmented flow to an electrophoresis sampling channel by a shallow and hydrophilic extraction bridge that removes the entire aqueous droplet from the oil stream. With this approach, temporal resolution was 35 s and independent of distance between sampling and analysis. Electrophoretic analysis produced separation with 223,000 +/- 21,000 theoretical plates, 4.4% RSD in peak height, and detection limits of 90-180 nM for six amino acids. This performance was made possible by three key elements: (1) reliable transfer of plug flow to a glass chip; (2) efficient extraction of aqueous plugs from segmented flow; (3) electrophoretic injection suitable for high efficiency separation with minimal dilution of sample. The system was used to detect rapid concentration changes evoked by infusing glutamate uptake inhibitor into the striatum of anesthetized rats. These results demonstrate the potential of incorporating segmented flow into separations-based sensing schemes for studying chemical dynamics in vivo with improved temporal resolution.