We developed analytical methods for monitoring carbon translocation and nitrogen fixation in intact plants using short-lived radioactive tracer gas and the positron-emitting tracer imaging system (PETIS). In the analysis of carbon translocation, we fed 11C (half life: 20.4 min)-labeled radioactive carbon dioxide gas to leaf blades of rice plants, and serial images of 11C-photoassimilate were obtained non-invasively using PETIS. In order to understand source-sink relations, we manipulated source and sink strength by treating tested rice plants with p-chlorobenzenesulfonic acid (PCMBS), an inhibitor of sucrose transporters. We developed an analytical algorithm to estimate the velocity of 11C-photoassimilate flow from the serial images. As a result, a decrease in the velocity after the manipulation was successfully detected. In the analysis of nitrogen fixation, we newly developed a rapid method to produce and purify 13N (half life: 10.0 min)-labeled radioactive nitrogen gas and fed the gas to the underground part of nodulated soybean plants. Serial images of distribution of 13N were obtained and obvious signal of 13N was observed at the nodules. To our knowledge, this is the first example of real-time imaging of nitrogen fixation in an intact plant.