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Abstract Background Archival tags have been used on fish for a number of years to measure temperature, pressure and salinity, among other parameters. Measurements of heart rate in fish can be used in a wide variety of biological and ecological studies, e.g., for evaluating short- and long-term effects of stressful conditions involved with fishing and farming practices, or events that are non-related to human activity, such as predator–prey interactions. Furthermore, if a relationship between temperature, heart rate and metabolic rate has been established there are potentials to establish long-term bioenergy models that include seasonal effects on feeding, locomotion, spawning and migration. However, heart-rate measurements in fish have been difficult to conduct in the wild due to lack of commercial availability, large size of the recording systems, difficulties with proper placement of external electrodes and restriction in setup with external systems. This work presents a validation of a commercial ECG (Electrocardiogram)-derived heart rate data logger on farmed Atlantic cod. This validation focuses on assessing the logger’s signal processing algorithm and recording quality. Results The eight fish studied showed both individual periodical variation, as well as individual baseline variation of the heart rate during the experimental period. Mean heart rate ranged from 29.9 ± 6.3 to 48.3 ± 4.9 bpm, at 10.2 ± 0.1 °C. This is comparable with previous research on Atlantic cod. The loggers were set up to record heart rate and temperature every 5 min and to store the ECG records used to calculate the heart rate every 30 min. The quality index (QI), which is an algorithmic assigned value of the quality of the ECG, was used to filter the data set eliminating a total of 21,643 measurements (19% of the recorded heart rate data). It was possible to manually calculate 18,490 out of 19,042 ECG records (97%). Conclusions This study presented a validation of using a commercial implantable data logging device in Atlantic cod that records ECG, and can calculate both heart rate, and a novel quality index for the ECG record with an on-board algorithm.