The aim of the study was to investigate the effect of lameness and specific causes of lameness on standing time, number of lying bouts and test day yield (TDY) in cows at pasture and cows which were housed. Data were collected from 200 cows from 10 farms where cows were at pasture and 200 cows from 10 farms where they were housed. Each farm was visited twice over 3 days between May and August (autumn and winter) of 2009. At the first visit, 10 lame cows, all with locomotion score (LS) 3, and 10 non-lame cows, all with LS 1, were selected per farm. Electronic data loggers were positioned on one hind leg of each cow to record standing time and transitions. These were removed 3 days later at the second visit. There was no significant difference in standing time between housed and pasture-based cows but lame cows stood for a mean 1.75 (SE 0.36) h/day less than non-lame cows in both systems. Cows with sole damage, wall damage, misshapen feet and infectious lameness all stood for less time than non-lame cows. Housed cows had a mean 1.4 more lying bouts per day than cows at pasture. Lame cows at pasture had 1.2 more lying bouts per day than non-lame cows but housed lame cattle had 0.8 fewer lying bouts than non-lame housed cattle, so overall the number of lying bouts in lame cows, housed or at pasture, was similar. The only lesion associated with a change in the number of lying bouts was sole damage with a mean 1.1 more lying bouts per day across systems than non-lame cows. Lame cows had lower TDY than non-lame cows and TDY was reduced more in lame cows when TDY was greater. In conclusion, standing times were similar in cows at pasture and in housed cows, but lying bouts were different. However, given the associations between standing time, lying bouts and TDY the results might be most strongly influenced by TDY, rather than system. Future studies investigating the impact of lameness on cow behaviour by system in cows with similar and a range of TDY would be informative.