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The aim of this study was to explore whether, during automatic milking, milking interval or its variation is related to somatic cell count (SCC), even when corrected for effects of production, lactation stage, and parity. Data on milking interval and production level were available from the automatic milking systems of 151 farms. Data on SCC, parity, and lactation stage were derived from dairy herd improvement records of the same farms. Mainly due to incomplete records, data of 100 farms were used in the final analysis. For every cow, only 1 test day was used in the final analysis. Milking interval, the coefficient of variation of milking interval, production rate, the difference in production rate between short- and long-term, parity, days in milk, and some biologically relevant interactions were used in a linear mixed model with farm as random variable to assess their association with log10-transformed SCC. None of the interactions was significantly related to SCC, whereas all main effects were, and thus, stayed in the final model. The effect of milking interval was, although significant, not very strong, which shows that the effect of milking interval on SCC is marginal when corrected for the other variables. The variation in milking intervals was positively related with SCC, showing that the variation in milking interval is even more important than the milking interval itself. In the end, this study showed only a limited association between milking interval and SCC when milking with an automatic milking system.