In rodents, cage cleaning increases cardiovascular and behavioural activity for several hours, which are commonly interpreted as stress responses. In mice, post-cleaning activity also includes aggression, which can cause serious injuries. This study was part of a long-term investigation into the effects of cage cleaning frequency on rat behaviour and welfare. Here we aimed to ascertain whether post-cleaning activity is stress- or aggression-related, thereby leading to recurrent acute reductions in welfare, or simply a result of non-aversive stimulation. Male Wistar (n = 160) and Sprague–Dawley (n = 160) rats, kept in four animal units, had their cages cleaned twice per week, once per week or once per fortnight, and were kept on one of two types of bedding. Behaviours were recorded in detail before and after cage cleaning for 20 weeks, as was the aversion-related Harderian gland secretion, chromodacryorrhoea (‘red tears‘). Cage cleaning caused decreased resting and increased feeding, walking, bedding manipulation and sheltering for at least 30 min after the disturbance. Skirmishing also increased markedly for 15 min after cleaning, but decreased thereafter to below baseline levels. Unlike in mice, all skirmishing was non-injurious and play-like. The frequency of cage cleaning did not affect the magnitude of this skirmishing peak, but rats that had their cages cleaned more frequently settled more quickly after cleaning. Surprisingly, chromodacryorrhoea decreased after cage cleaning; this could mean that rats find soiled cages stressful or alternatively, like many disturbances, cage cleaning might provoke frequent, curtailed bouts of grooming, thereby removing the secretion. Rats also manipulated aspen bedding more than paper bedding. Overall, we found no evidence that cage cleaning caused rats any acute decrease in welfare — a finding consistent with additional data we have obtained on the lack of preference by rats for soiled over clean cages, and a lack of long-term, behavioural and physiological responses to being cleaned frequently or infrequently.