Metal-organic frameworks (MOFs) offer disruptive potential in micro- and optoelectronics because of the unique properties of these microporous materials. Nanoscale patterning is a fundamental step in the implementation of MOFs in miniaturized solid-state devices. Conventional MOF patterning methods suffer from low resolution and poorly defined pattern edges. Here, we demonstrate the resist-free, direct X-ray and electron-beam lithography of MOFs. This process avoids etching damage and contamination and leaves the porosity and crystallinity of the patterned MOFs intact. The resulting high-quality patterns have excellent sub-50-nm resolution, and approach the mesopore regime. The compatibility of X-ray and electron-beam lithography with existing micro- and nanofabrication processes will facilitate the integration of MOFs in miniaturized devices. The low dielectric constants and high porosity of MOFs are of interest for applications in electronics and sensors, but patterning techniques for these materials are in their infancy. Here, direct X-ray and electron-beam lithography at sub-50-nm resolution are reported that leave porosity and crystallinity intact.