Research has indicated that chronic stress can reduce sleep quality and quantity. Yet there has been little investigation into whether husbandry procedures carried out during an animal's normal sleeping period affect subsequent sleep behaviour and welfare. We housed 48 rats in enriched cages containing four rats, in either a light phase treatment (LPT) (n=6 cages) or a dark phase treatment (DPT) (n=6 cages). Rats in the LPT were exposed to husbandry procedures (e.g. weighing, cleaning) during the light phase when we would expect them to be inactive/sleeping, three times every week. DPT rats experienced the same procedures, but during the dark phase when we would expect them to be active/awake. After five weeks, behaviour for all cages was sampled over 12h of both the light and dark phase. General health measures (e.g. body weight) were collected over the five weeks housing period, and organ weights (e.g. thymus) were recorded post-mortem. Principal component analyses yielded four factors, two of which revealed treatment differences. For one, loading positively on chromodacryorrhoea score and negatively on sleep, self-grooming and enrichment directed behaviour, LPT rats scored higher than DPT rats. The other loaded positively for relative thymus weight and activity and negatively for aggression and social interaction. DPT rats scored higher on this than LPT rats. LPT rats thus displayed indicators of reduced welfare (e.g. less sleep, elevated chromodacryorrhoea, lighter thymus glands, higher aggression) relative to DPT rats. Therefore, husbandry procedures applied in the dark rather than the light phase might improve the welfare of laboratory rats.