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Ultra- and circadian activity rhythms of animals can provide important insights into animal welfare. The consistency of behavioral patterns is characteristic of healthy organisms, while changes in the regularity of behavioral rhythms may indicate health and stress-related challenges. This pilot study aimed to examine whether dairy cows in free-stall barns with an automatic milking system (AMS) and free cow traffic can develop ultra- and circadian activity rhythms. On 4 dairy farms, pedometers recorded the activity of 10 cows each over 28 days. Based on time series calculation, the Degree of Functional Coupling (DFC) was used to determine the cows' activity rhythms. The DFC identified significant rhythmic patterns in sliding 7-day periods and indicated the percentage of activity (0–100%) that was synchronized with the 24-h day-night rhythm. As light is the main factor influencing the sleep-wake cycle of organisms, light intensity was recorded in the AMS, at the feed alley and in the barn of each farm. In addition, feeding and milking management were considered as part of the environmental context. Saliva samples of each cow were taken every 3 h for 1 day to determine the melatonin concentration. The DFC approach was successfully used to detect activity rhythms of dairy cows in commercial housing systems. However, large inter- and intra-individual variations were observed. Due to a high frequency of 0 and 100%, a median split was used to dichotomize into “low” (<72.34%) and “high” (≥72.34%) DFC. Forty percent of the sliding 7-day periods corresponded to a low DFC and 50% to a high DFC. No DFC could be calculated for 10% of the periods, as the cows' activity was not synchronized to 24 h. A generalized linear mixed-effects model revealed that the DFC levels were positively associated with a longer milking interval and a higher amount of daytime activity and negatively associated with higher number of lactations. The DFC is a novel approach to animal behavior monitoring. Due to its automation capability, it represents a promising tool in its further development for the purpose of longitudinal monitoring of animal welfare.