This study evaluated the effect of 2 dairy cow housing systems on cow locomotion, immune status, and expression of genes associated with lameness during the dry and periparturient periods. Cows were assigned to freestall housing with either rubber (RUB; n = 13) or concrete (CON; n = 14) at the feed-bunk and alley immediately after their first calving, and managed on this system during all subsequent lactations. At dry off, cows were moved to a straw bedded-pack dry cow pen, and remained there until about 2 d before subsequent calving. To investigate whether greater exposure to RUB or CON increased the differences between cows on each treatment, cows at the end of either their first (n = 16) or second (n = 11) lactations were included in the experiment. Locomotion scores and blood samples were obtained at -60 (beginning of the dry period), -30, 0 (after calving), +10 and +18 d relative to calving. Leukocyte counts were obtained by using an automated cell counter. Phagocytic activity, and cells positive for CD14 and CD18 expression were measured by flow cytometry using labeled microbeads and antibodies. Expression of tachikinin 1(TAC1), histamine receptor 1 (H1), and metalloproteinase (MMP)13 in blood leukocytes was estimated using quantitative real-time PCR. Treatment effects were determined using a repeated measures model. Provision of rubber flooring did not improve dairy cow locomotion during the subsequent study period. However, time relative to calving had an effect on locomotion score and speed, which were worst on d 0, probably because of the discomfort associated with calving. An interaction occurred between treatment and time for neutrophil and lymphocyte counts. The RUB cows had greater neutrophil and lesser lymphocyte numbers postpartum than CON. These cows also had more cells positive for CD14 postpartum compared with prepartum. Moreover, RUB cows showed upregulation of MMP13 and TAC1 compared with CON. These genes are associated with lameness and pain detection respectively. Greater neutrophil to lymphocyte ratios and CD14 expression are associated with physiological stress or with activated immunity. Rubber flooring is associated with an increase in activity and standing. This may have resulted in indications of physiological stress and upregulation of genes associated with lameness and pain for RUB cows. However, this study did not take into account the long-term effects of concrete or rubber flooring; for instance, occurrence of lameness or survivability within the herd.