Enteric methane emission from ruminants contributes substantially to the greenhouse effect. Few studies have focused on the genetic variation in enteric methane emission from dairy cattle. The objective of this study was to estimate the heritability for enteric methane emission from Danish Holstein cows. On a total of 683 dairy cows a Fourier Transformed Infrared (FTIR) measuring unit was used to make large scale individual methane emission records. The cows were measured in 7 herds during their visits to automatic milking systems (AMS). The FTIR unit air inlet was mounted in the front part of an AMS close to the cows head for 7 days, recording continuously every 5 seconds. The phenotype analysed was the mean methane to carbon dioxide ratio across visits during the measuring period, as this ratio reflects the proportion of the metabolisable energy exhaled as methane. The statistical linear model included fixed effects of herd, month, days in milk, lactation number, and random effects of animal and residual. Variance components were estimated in an animal model design using a pedigree containing 9661 animals. The heritability of the methane to carbon dioxide ratio was moderate (0.21). The results from this study suggest that individual cow’s methane emission can be accurately measured using FTIR equipment and that the trait is heritable. The data can be used for both management and genetic analysis and opens for future studies on the correlation between methane emission and other traits of economic importance in the breeding goal as well as the possibility to use methane as an indicator of feed efficiency. It is concluded that FTIR breath analysis is effective for measuring GHG emissions and may find further applications with a wider panel of gases including acetone and its relation to ketosis.