Current methods of identifying and analysing behavioural signs of pain in mice are highly time consuming and labour intensive. HomeCageScan (HCS) is an automated analysis system that may offer an alternative to manual scoring. Thirty-two male mice undergoing vasectomy were filmed before and at 1 h following surgery. Their behaviour was analysed by manual scoring and using an automated system (HCS; Clever Systems Inc.). The methods were compared using Bland–Altman plots, indicating a good level of agreement between the two methods for some behaviours. Other behaviours assessed showed HCS to over- or under-estimate the frequency or duration, however, when analysed using the Bland–Altman approach the two methods of analysis were still deemed interchangeable. This study has indicated that the automated analysis system may be appropriate for rapid analysis of behaviour changes in mice in some areas of biomedical research.