We have an ethical and scientific obligation to Refine all aspects of the life of the laboratory-housed dog. Across industry there are many differences amongst facilities, home pen design and husbandry, as well as differences in features of the dogs such as strain, sex and scientific protocols. Understanding how these influence welfare, and hence scientific output is therefore critical. A significant proportion of dogs' lives are spent in the home pen and as such, the design can have a considerable impact on welfare. Although best practice guidelines exist, there is a paucity of empirical evidence to support the recommended Refinements and uptake varies across industry. In this study, we examine the effect of modern and traditional home pen design, overall facility design, husbandry, history of regulated procedures, strain and sex on welfare-indicating behaviours and mechanical pressure threshold. Six groups of dogs from two facilities (total n=46) were observed in the home pen and tested for mechanical pressure threshold. Dogs which were housed in a purpose-built modern facility or in a modern design home pen showed the fewest behavioural indicators of negative welfare (such as alert or pacing behaviours) and more indicators of positive welfare (such as resting) compared to those in a traditional home pen design or traditional facility. Welfare indicating behaviours did not vary consistently with strain, but male dogs showed more negative welfare indicating behaviours and had greater variation in these behaviours than females. Our findings showed more positive welfare indicating behaviours in dogs with higher mechanical pressure thresholds. We conclude that factors relating to the design of home pens and implementation of Refinements at the facility level have a significant positive impact on the welfare of laboratory-housed dogs, with a potential concomitant impact on scientific endpoints.