Over 234,000 rats were used in regulated procedures in the UK in 2014, many of which may have resulted in some degree of pain. When using animals in research, there is an ethical and legal responsibility to alleviate or at least reduce pain to an absolute minimum. To do this, we must be able to effectively assess pain in an accurate and timely manner. The Rat Grimace Scale (RGS) is a pain assessment tool, which is suggested to be both accurate and rapid in pain assessment. Many procedures involve the use of general anaesthesia. To date, the effects of anaesthesia on the RGS have not been assessed, limiting its potential utility for assessing pain following anaesthesia. Forty-eight Lister hooded rats were used in this study (24 in part A and 24 in a separate part B). Rats were randomly assigned to one of two treatment groups in part A; short duration isoflurane exposure, short duration control exposure (air) and one of two treatment groups in part B; surgical duration isoflurane exposure or surgical duration control exposure (oxygen). Rats were placed into an anaesthetic induction chamber and isoflurane, or control gas piped into the chamber for either 4 (short duration exposure) or 12 minutes (surgical duration exposure). Following recovery, photographs of the rats' faces were taken and then scored blindly using the RGS. Short duration isoflurane anaesthesia had no effect on RGS scores. However, when rats are anaesthetised for a longer duration, akin to a simple routine surgical procedure, the RGS score increases significantly and this increase remains on repeated exposure to this duration of anaesthesia over a 4-day period. This should be accounted for when using the RGS to assess pain in rats in the immediate time period following procedures involving the use of isoflurane anaesthesia.