The 'subcutaneous glucose monitoring system' (SCGM) is based on microdialysis and allows continuous glucose monitoring in abdominal adipose tissue of diabetic patients up to 5 days. In the current in vivo study we compared the SCGM system with a commercially available needle type glucose sensor during an oral glucose tolerance test (OGTT) and during physical exercise. The SCGM had a good in vivo performance that was comparable to the needle type sensor. The inherent safe measuring technology of microdialysis and sensor stability of the SCGM makes it a likely candidate for online glucose measurement in diabetic patients. However, the overall system configuration is too bulky to wear comfortably and the measured values have a time lag of 35 min. The SCGM system will be the base for the future development of a miniaturized integrated microdialysis sensor system using labon-a-chip technology.