International environmental agreements have led to the need to reduce methane emission by dairy cows. Reduction could be achieved through selective breeding. The aim of this study was to quantify the genetic variation of methane emission by Dutch Holstein Friesian cows measured using infrared sensors installed in automatic milking systems (AMS). Measurements of CH4 and CO2 on 1508 Dutch Holstein Friesian cows located on 11 commercial dairy farms were available. Phenotypes per AMS visit were the mean of CH4, mean of CO2, mean of CH4 divided by mean of CO2, and their log10-transformations. The repeatabilities of the log10-transformated methane phenotypes were 0.27 for CH4, 0.31 for CO2, and 0.14 for the ratio. The log10-transformated heritabilities of these phenotypes were 0.11 for CH4, 0.12 for CO2, and 0.03 for the ratio. These results indicate that measurements taken using infrared sensors in AMS are repeatable and heritable and, thus, could be used for selection for lower CH4 emission. Furthermore, it is important to account for farm, AMS, day of measurement, time of day, and lactation stage when estimating genetic parameters for methane phenotypes. Selection based on log10-transformated CH4 instead of the ratio would be expected to give a greater reduction of CH4 emission by dairy cows.