Application accuracy is a crucial factor for stereotactic surgical localization systems. The different qualities of medical images can produce different influences on the application accuracy. However there are a lot of factors that can have an effect on the application accuracy. In this study, we compared the influences of different section thickness of MRI and CT images on the application accuracy during image-guided surgery. An implantable frameless marker system was used. CT scans were taken using 2 kinds of thickness, 1 and 2 mm, and with 2 resolution 256 X 256, 512 X 512. T1 weighted MRI images were used with 3 kinds of thickness, 1 and 3 and 10mm. The IR tracking systems and the Neurosurgery Planning System software were used to do image registration and intraoperative digitization. The differences among the mechanical measurements, image digitization from the computer and the measurement through the tracking systems were compared. The mechanical measurement was used as the most accurate measurement. A statistical study was used to analyze the results. In the CT group, there was a significant difference between 1mm and 2mm sections. There was also a difference found between the 256 X 256 and 512 X 512 image quality groups. In the MRI group, there was a significant difference between 10mm and 1mm or 3mm sections, but no difference between 1mm and 3mm sections. When compares CT and MRI with 1mm thickness, there was no significant difference. For the evaluation of the application accuracy during image-guided surgery, the quality of the medical image is an important factor to be dealt with. The thickness of section is usually used factor to analyze the influence. It is commonly accepted that the thinner the thickness, the better the application accuracy. However there is a limitation. Our results showed that for CT images the thickness when reduced from 2mm to 1mm can still significantly improve the application accuracy. But in MRI image when the thickness were reduced from 3mm to 1mm, the application accuracy remained the same. These results may reflect the difference of machines producing these medical images. The quality of medical images do have influences on the application accuracy during image guided surgery.