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RATIONALE: The stable carbon isotope ratio (13C/12C or δ13C value) of methane (CH4) produced in methanogenic environments contains information about primary source material, CH4 production pathways, degree of oxidation, and transport. However, the availability of δ13C-CH4 data is severely limited because isotope analysis methods are low throughput, owing primarily to the need for manual processing steps. High-throughput, fully automated measurement is necessary to facilitate the use of the δ13C signature in understanding CH4 biogeochemistry. METHODS: We modified a conventional continuous-flow (CF) gas chromatography/combustion/isotope ratio mass spectrometry (IRMS) instrument system by incorporating (i) automated sample injection, (ii) a newly developed temperature-control unit for preconcentration and cryofocus traps, and (iii) an automatic system for liquid-nitrogen refilling. The system, which could run unattended for 1 day, was used to obtain δ13C-CH4 data for CH4 samples collected from an irrigated rice paddy with an automated closed-chamber system. RESULTS: Using the fully automated CF-IRMS system, we measured δ13C-CH4 data for 77 samples during a 21.5-h continuous run (17 min per sample) with high precision (1σ = 0.11‰, reproducibility) and moderate consumption of liquid nitrogen (11 L). Application of the system to CH4 samples obtained from the rice paddy revealed distinct seasonal and diurnal variations in δ13C values with the highest temporal resolution ever reported. CONCLUSIONS: A fully automated, high-throughput system for the measurement of δ13C-CH4 values was developed and used to analyze air samples obtained from a rice paddy. Our results demonstrate the high potential of this system for obtaining δ13C data useful for process-level understanding of CH4 biogeochemistry with respect to spatiotemporal variation of CH4 sources and how that variation is affected by environmental and management factors. [ABSTRACT FROM AUTHOR]