We present a novel alignment system for x-ray lithography. A linear Fresnel zone plate, defined on the mask, is used to focus a laser beam on a wafer mark (a series of dots). A fast electro-optic modulator is used to make the laser beam hop between two positions at the mark edges. The light diffracted by the periodic mark is measured at each position and a misalignment signal is originated when the mark is not illuminated equally in the two states. A signal that is proportional to the misalignment is generated when the error is within the alignment range (±0.2 μm); outside that range a capture signal is present as long as the beam is on the mark, which would be typically 2–4 μm wide. The method is highly sensitive with resolution in excess of 0.003 μm, has a wide capture range, no moving parts, and is suitable for real-time alignment during exposure. Sensitivity to gap changes is highly reduced, making the system ideal for synchrotron-based x-ray lithography aligners.