Pressure balanced downhole connections. A well system includes a well tool, a conduit assembly connected to the well tool, the conduit assembly including a conduit and a line positioned within the conduit, the line being connected to the well tool for operation of the well tool, and a device for equalizing pressure between an interior and an exterior of the conduit, the device being positioned downhole. A method of isolating a line in a subterranean well from well fluids in the well includes the steps of: connecting a conduit assembly to a device for equalizing pressure between an interior and an exterior of the conduit assembly, the conduit assembly including a line installed within a conduit; and positioning the conduit assembly and pressure equalizing device in the well.