In this study, flow characteristics and thermal performance of the micro pulsating heat pipe (MPHP) with same hydraulic diameter (0.57 mm) but different shaped cross-sections were experimentally investigated. Two types of micro pulsating heat pipe which were fabricated using a micro-electromechanical fabrication technique were evaluated: a circular channel MPHP and a square channel MPHP. Each channel was etched on a silicon wafer with thickness of 1mm. Ethanol was used as a working fluid and the MPHP was tested in vertical orientation. Pyrex glass is bonded to silicon by anodic bonding to confirm the in-ternal flow pattern of the square and circular channel MPHP. The flow visualization using high speed camera showed the different flow pattern and amplitude which are an important parameter of thermal performance on pulsating mode. The minimum thermal resistance of the square channel MPHP is 3.3 K/W, which is about 3.2 times smaller than the circular channel MPHP. The square channel MPHP achieved maximum effective thermal conductivi-ty of 727 W/moK which is the 4.9 times higher than thermal conductivity of silicon (k = 150 W/moK). For performance comparison, the experimental measurements were conducted on the MPHPs by using infrared camera. The square channel MPHP was better thermal perfor-mance than the circular MPHP because corners in square channel MPHP delayed the com-plete dry out and acted as the nucleation cavities.