To get high quality magnetic resonance (MR) micro-images for the physiological and anatomical investigation of tree stems, the imaging with various combinations of parameters was tested on a Signa VH/i 3.0 T MR imaging system (General Electric Medical Systems). Proton density and T2 weighted spin echo (SE) sequences are commonly used to detect areas with abundant water. Cambial zone and the area consisting of water-filled conduits looked whitish in the MR images of healthy Pinus densiflora and Quercus serrata stems that were obtained by these sequences. In the MR images of diseased P. densiflora that had been inoculated with a wilt pathogen, Bursaphelenchus xylophilus, the area dehydrated as a result of embolism appeared pitch-black. In the images of diseased Quercus crispula saplings, that had been inoculated with the wilt pathogen Raffaelea quercivora, the dehydrated xylem was shown as a dark area. The T1 weighted SE or gradient echo (FSPGR) sequence, that is used to detect fat and protein distribution, provided high intensity MR signals for the pathogenic heartwood and necrotic areas resulting from fungal activity. The resolution of MR images obtained by SE sequences was estimated 100–150 μm from the FOV and image size. The data sets obtained by the FSPGR sequence that consist of 0.8 mm thick serial sections enables the three-dimensional analysis of the affected area. This technique is helpful for detecting the water distribution and areas affected by pathogenic microorganisms in living tree stems.