Development of a compact fluorescence-based detection system for use in a micro-analytical system, such as a point-of-care diagnostic system, often requires a multi-channel microfluidic chip system. Since the materials used for microfluidic chips usually are transparent in the visible region and have a refractive indices higher than that of air or the surrounding environment, the fluorescence emission and scattered excitation light can propagate through the chip. We observed that such propagation can cause cross-talk between adjacent channels, and may become the major source of noise in the system and/or photo bleach the fluorescent samples in the adjacent channels, particularly for the small distances between the channels found in microfluidic chips, usually in order of several micro m. We monitored this cross-talk using fluorescein as a fluorescent sample and Mylar sheeting as a microfluidic chip material. We then discuss how this cross-talk can be avoided using a simple, inexpensive and effective method.