Daily handling of preweanling rats reduces their adult anxiety. Even routine cage-cleaning, involving handling, reduces adult anxiety compared with controls. Cage-cleaning regimes differ between animal breeders, potentially affecting rodent anxiety and experimental results. Here, 92 adult male rats given different cage-cleaning rates as pups, were compared on plus-maze, hyponeophagia, corticosterone, and handling tests. They were pair-housed and half were tailmarked for identification. Anxiety/stress profiles were unaffected by cage-cleaning frequency, suggesting that commercial-typical differences in husbandry contribute little variance to adult rat behavior. However, delivery batch affected some elevated plus-maze measures. Also, tail-marked rats spent three times longer on the plusmaze open arms than their unmarked cagemates, suggesting reduced anxiety, yet paradoxically they showed greater chromodacryorrhoea responses to handling, implying increased aversion to human contact. A follow-up study showed that rats avoided the odor released from the marker pen used. Thus, apparently trivial aspects of procedure can greatly affect experimental results.