The operation of solar cells and light-emitting displays strongly depends on the properties of the interfaces between positive hole-carrying and negative electron-carrying regions of the devices. This is particularly the case when the charge carrying materials are organic semiconductors. The boundary interfacial regions between different organic semiconductors in these devices are generally difficult to characterize, as they are usually buried under the surface or exist as an irregular “bulk heterojunction.” Using a novel fluorinated barrier layer-based lithographic technique, we fabricated individual positive-negative (pn) junctions between pairs of organic semiconductors side-by-side, allowing the first observation of electrical properties at an interface between hole- and electron-carrying organic semiconductors while the interfaces were active in devices. We find that the diode characteristics of the device (current output and the ratio of currents in the p-n and n-p directions) are consistent with the changes in the surface potentials near the junction, and the current-voltage curves and junction potentials are strongly and self-consistently modulated by a third, gate electrode. The generality of our technique makes this an attractive method to investigate the physics of organic semiconductor junctions. The lithographic technique is applicable to a wide variety of soft material patterns. The observation of built-in potentials makes an important connection between organic junctions and textbook descriptions of the charge distributions in standard inorganic devices. Finally, these kinds of potentials may prove to be controlling factors in charge separation efficiency in organic solar cells used for the generation of electrical power.