Integrated microfluidic systems coupled with electrophoretic separations have broad application in biologic and chemical analysis. Interfaces for the connection of various functional parts play a major role in the performance of a system. Here, we developed a rapid prototyping method to fabricate monolithic poly(dimethylsiloxane) (PDMS) interfaces for flow-gated injection, online reagent mixing, and tube-to-tube connection in an integrated capillary electrophoresis (CE) system. The basic idea was based on the properties of PDMS: elasticity, transparency, and suitability for prototyping. The molds for these interfaces were prepared by using commercially available stainless steel wires and nylon lines or silica capillaries. A steel wire was inserted through the diameter of a nylon line and a cross format was obtained as the mold for PDMS casting of flow gates and 4-way mixers. These interfaces accommodated tubing connection through PDMS elasticity and provided easy visual trouble shooting. The flow gate used smaller channel diameters, thus reducing flow rate by 25-fold for effective gating compared with mechanically machined counterparts. Both PDMS mixers and the tube-to-tube connectors could minimize the sample dead volume by using an appropriate capillary configuration. As a whole, the prototyped PDMS interfaces are reusable, inexpensive, convenient for connection, and robust when integrated with the CE detection system. Therefore, these interfaces could see potential applications in CE and CE-coupled systems.