Measuring soft tissue thickness is an important step in rheumatoid disease research. The severity of mouse footpad swelling can be used as an indicator of disease progression. A noncontact footpad thickness assay, simplified geometry measurement system (SGMS), was developed that was able to reduce both intra- and interobserver variances during measurements. Three materials with five objects each were used in this study: hard blocks, soft sponges and mouse footpads. Thicknesses were measured using calipers or the SGMS. In the measurement of the hard block, there was no difference in measurement errors between calipers and SGMS. For the mouse footpad thickness, there was significant difference in intraobserver variances among three observers and a significant difference of interobserver variances between calipers and SGMS. In conclusions, this noncontact assay is reliable and highly reproducible for the assessment of inflammatory reactions when results are expressed as a gradual increase in footpad thickness.