In this paper we describe a multijunction microfluidic device for the injection of a substrate into an array of preformed plugs carried by an immiscible fluid in a microchannel. The device uses multiple junctions to inject substrate into preformed plugs without synchronization of the flow of substrate and the array of preformed plugs of reagent, which reduces cross-contamination of the plugs, eliminates formation of small droplets of substrate, and allows a greater range of injection ratios compared to that of a single T-junction. The device was based on a previously developed physical model for transport that was here adapted to describe injection and experimentally verified. After characterization, the device was applied to two biochemical assays, including evaluation of the enzymatic activity of thrombin and determination of the coagulation time of human blood plasma, which both provided reliable results. The reduction of cross-contamination and greater range of injection ratios achieved by this device may improve the processes that involve addition and titration of reagents into plugs, such as high-throughput screening of protein crystallization conditions.In this paper we discuss a physical model of multiphase fluid flow 1,2 during injection of a stream into droplets and the use of this model to design and validate a multijunction microfluidic injector for reliable addition of a substrate into an array of preformed plugs containing reagents. This model has been presented previously for multiphase separation, 1,2 and we used it to describe the related process of injecting reagents into droplets. Microfluidic systems are attractive for miniaturizing laboratory techniques, 3-8 and systems with multiphase flows are useful for compartmentalizing reagents, enhancing mixing, and reducing dispersion but require improved understanding and control. 2,3,6,9-13 In plug-based systems, nanoliter or picoliter droplets are formed within microchannels and carried by an immiscible fluid. 14-16 Each plug contains multiple reagents and can act as a microreactor. 13,17-21 For chemical and biological reactions and analysis, multiple substrates and reagents must be introduced into plugs. Introducing multiple reagents as a plug is forming can be done simply by relying on laminar flow of several streams containing reagents. 13 However, reliable addition of a substrate to preformed plugs is more challenging.Injection into preformed plugs may improve a number of processes such as protein crystallization, 22 synthesis of particles, 23 biological assays, 22 combinatorial chemistry, 24 and chemical synthesis with one or multiple steps. 25,26 In a T-junction, substrate is injected from the side channel into preformed plugs traveling in the main channel ( Figure 1A). Three problems were identified for injection using a T-junction: (i) Cross-contamination between plugs occurred when the substrate stream picked up reagents from a preformed plug and