Wettability is a critical parameter in micro-scale two-phase system. Several previous results indicate that wettability has influential affect on two-phase flow pattern in a microchannel. However, previous studies conducted using circular microtube, which was made by conventional fabrication techniques. Although most applications for micro thermal hydraulic system has used a rectangular microchannel, data for the rectangular microchannel is totally lack. In this study, a hydrophilic rectangular microchannel was fabricated using a photosensitive glass. And a hydrophobic rectangular microchannel was prepared using silanization of glass surfaces with OTS (octa-dethyl-trichloro-siliane). Experiments of two-phase flow in the hydrophilic and the hydrophobic rectangular microchannels were conducted using water and nitrogen gas. Visualization of twophase flow pattern was carried out using a high-speed camera and a long distance microscope. Visualization results show that the wettability was important for two-phase flow pattern in rectangular microchannel. In addition, two-phase frictional pressure drop was highly related with flow patterns. Finally, Two-phase frictional pressure drop was analyzed with flow patterns.