A small angle x-ray diffraction scattering system has a vertical orientation, allowing for simplified analysis of liquid samples. The system may function in a beam-up or a beam-down configuration. An x-ray source provides an initial x-ray beam that is directed vertically along a primary beampath to a sample located on a sample support. The small angle scattered x-ray energy travels through a secondary beampath to a detector. The primary and secondary beampaths may be evacuated and separated from a sample chamber by fluid seals. Beam conditioning optics and a collimator may be used in the primary beampath, and a beamstop used in the secondary beampath. The sample chamber may have a microscope or camera, which may be movable, for observing the sample, and a translation stage for moving the sample in at least two dimensions.