Improved system and method of X-ray laser microscopy that combines information obtained from both X-ray diffraction and X-ray imaging methods. At least one sample is placed in an ultra-cold, ultra-low pressure vacuum chamber, often using a sample administration device configured to present a plurality of samples. The sample is exposed to brief bursts of coherent X-ray illumination, often further concentrated using X-ray mirrors and pinhole collimation methods. Higher resolution data from the samples is obtained using hard X-ray lasers, such as free electron X-ray lasers, and X-ray diffraction methods. Lower resolution data from the same samples can be obtained using any of hard or soft X-ray laser sources, and X-ray imaging methods employing nanoscale etched zone plate technology. In some embodiments both diffraction and imaging data can be obtained simultaneously. Data from both sources are combined to create a more complete representation of the samples.