To maintain and enhance cow productivity and welfare, it is important that we can accurately assess and understand how cows respond to the physiological demands of gestation and lactation. Several methods have been developed for assessing the physiological responses to stressors and for detecting distress in cattle. Heart rate (HR) variability (HRV) is a non-invasive measure of autonomic nervous system activity and consequently a component of the physiological response to stress. In cattle, HRV has been successfully used to measure autonomic responses to a variety of health conditions and management procedures. The objectives of this study were to determine whether, among commercial Holstein Friesian cows and across farms, relationships exist between cow-level factors, HR and HRV. HRV parameters were compared with production records for 170 randomly selected, Holstein-Friesian-cows on 3 commercial dairy farms. Production data included parity, days in milk (DIM), milk yield, somatic cell count (SCC), % butterfat and protein, body condition score (BCS) and genetic indices. Fixed-effect, multivariable linear regression models were constructed to examine the association between cow-level variables and HRV parameters. Statistically significant relationships were found between HR and farm, temperature and BCS, and between HRV parameters and farm, rectal temperature, BCS, DIM, and percentage butterfat. Given the significant association between farms and several of the indices measured, it is recommended that care must be taken in the interpretation of HRV studies that are conducted on animals from a single farm. The current study indicated that within clinically normal dairy cattle HRV differed with the percentage of butterfat and BCS. Based on the relationships reported previously between HRV and stress in dairy cattle these results suggest that stress may be increased early in lactation, in cows with BCS <2.75 that are producing a high percentage of butterfat milk. Future work could focus on the physiological mechanisms through which these factors and their interactions alter HRV and how such physiological stress may be managed within a commercial farm setting.