This study investigates the fluorogenic characteristics of the chitosan-genipin reaction for applications in microencapsulation research. Results showed that the chitosan-genipin reaction generated a colored and fluorescent product, with optimal excitation and emission wavelengths at 369 and 470 nm, respectively. Furthermore, it was found that reaction conditions affected the fluorescence intensity of the product. Mixture at the ratio of 4:1 (chitosan: genipin by weight) fluoresced the most. It also fluoresced stronger if the reaction occurred at higher temperature, with the intensity of 10.4 x 10(5) CPS at 37 degrees C, 5.9 x 10(5) CPS at 20 degrees C, and 2.5 x 10(5) CPS at 4 degrees C. As well, the fluorescence of the mixture developed gradually over time, attaining the emission maxima of 2.9 x 10(5), 7.6 x 10(5), and 10.0 x 10(5) CPS in 1, 6, and 18 h, respectively. Chitosan-coated alginate microcapsules were prepared without prior labeling, to which subsequent genipin treatment was applied in order to examine the potential of using genipin in microcapsule characterization. Chitosan bound to the alginate beads interacted with genipin, from which the resultant fluorescent signals allowed for clear visualization of the chitosan coating under confocal laser scanning microscopy. The relative fluorescence intensity across the chitosan membrane was found to be considerably higher than the controls (175 vs. 50). The membrane thickness measured was 29.2 +/- 7.3 microm. These findings demonstrate a convenient and effective way of characterizing chitosan-based microcapsules using genipin as a fluorogenic marker, a technique that will be useful in microcapsule research and other biomedical applications.