Mouse fibroblast cell line NIH3T3 cells were labeled with the heavy metal (silver and gold) and observed intracellular structure under an X-ray microscope. Microtubules, Golgi apparatus and early endosomes of NIH3T3 cells were stained with immuno-gold nanoparticles, and immuno-staining was intensified by silver or gold enhancement procedure. Using a transmission soft X-ray microscope beamline (BL12) at Ritsumeikan University SR center, we observed immuno-stained NIH3T3 cells with several wavelengths just below and above oxygen edge (λ = 2.32 nm). Using this method, cytoskeleton (microtubules) and organelles (Golgi apparatus and early endosomes) were successfully imaged with high resolution. Thus, immuno-gold silver and gold enhancement technique is useful for specific labeling of intracellular structure under an X-ray microscope.