Apparatus and methods for performing small angle X-ray scattering (SAXS) at low (cryogenic) temperatures for determining the structure of and changes in the structure of proteins, DNA, RNA, and other biological molecules and biomolecular assemblies and structures. A cryogenic, small angle X-ray scattering (SAXS) application sample holder, includes a sample cell including a base portion and at least two parallel walls disposed on the base, wherein the sample cell has a liquid volume capacity defined by the walls and the base portion of 0.001 to 10 microliters. A method for performing cryogenic SAXS on a sample includes the steps of providing a sample biomolecule solution containing an aqueous buffer, a biomolecule, and a cryoprotectant agent, wherein the cryoprotectant agent comprises up to 60% (w/w) of the biomolecule solution, and other known components as necessary to solubilize and stabilize the biomolecule, in a sample holder of claim 1, cryogenically cooling the sample solution in the sample holder at a rate equal to or greater than 100 K/sec without ice formation, and examining the cooled sample using small angle X-ray scattering by passing a beam of X-rays through the sample.