H2 clearance method in measuring regional cerebral blood flow (rCBF) on animals has been widely used in experimental research. It was found that 3% H2 which is lower than the lower concentration limit guarded against occurrence of explosion could be mixed with any concentration ratio of N2 to O2 without causing transient hypoxia as often found by inhaling 100% H2 and thus made clearance measurement more accurate and safe. Comparison studies between inhaling 100% H2 and 3% H2 as well as inhaling 3% H2 for 1-1.5 min and 3% H2 for 5 min were undertaken. Repeated measurements of 3% H2 clearance for 1.5 min further showed that clearance test using low H2 concentration for short term periods reflected better the rCBF of experimental animals.