Paper-based microfluidic patterns have been demonstrated in recent literature to have a significant potential in developing low-cost analytical devices for telemedicine and general health monitoring. This study reports a new method for making microfluidic patterns on a paper surface using plasma treatment. Paper was first hydrophobized and then treated using plasma in conjunction with a mask. This formed well defined hydrophilic channels on the paper. Paper-based microfluidic systems produced in this way retained the flexibility of paper and a variety of patterns could be formed. A major advantage of this system is that simple functional elements such as switches and filters can be built into the patterns. Examples of these elements are given in this study.