Times are constantly moving forward, and work is being modernised and made more efficient in all areas, not only agriculture. There has been a move towards collecting milk yield data from milking systems linked to computers for milk yield monitoring. However, it has been found that data from milking systems sometimes deviate from the data recorded manually on a personal digital assistant (PDA) in milk yield control. This work aimed to compare the milk yield data from the milking systems. Data was collected using a PDA as part of a milk yield check. The amount of milk from each cow’s milking was recorded manually by a currently calibrated measuring system. Data from the milking system were downloaded from Farmsoft, which the selected farms use for herd management. Comparisons were made for 90 dairy cows, with three lactations assessed. Differences between the milking system and milk recording data were confirmed on one of the three farms with greater than 5% probability. The average difference between farrowing was 4.2 kg, with a maximum deviation of 54.1 kg. These deviations may be caused by inappropriate cow identification equipment, poor configuration of different milking system technologies and computer programs, or less reliable milking system technology. Further research into the possible causes of poor identification and the acquisition of innovative animal identification technologies is recommended.