The objective of this study was to examine housing and management factors associated with clinical lameness in Holstein freestall housed dairy cattle across USA. Data were collected from 535 commercial freestall dairy farms from November 2012 to July 2017. Herd size averaged 1,434 (range 105–13,000) lactating cows. The high production Holstein pen was scored for locomotion (LS; 1 = normal gait, 5 = severely lame; clinically lame, LS ≥ 3), hock injuries (hair loss and/or swelling; %) and knee injuries (swollen; %). Accelerometers were placed on 40 randomly selected cows for pen 3 d averaged daily lying time. Lying time difference was calculated from longest and shortest 3 d averaged lying times of the pen. Lameness prevalence averaged (mean ± SD, %) 28.3 ± 13.2, pen lying time and pen lying time difference averaged (mean ± SD, h/d) 10.89 ± 1.12 and 8.79 ± 1.92, respectively. Hock and knee injuries averaged (mean ± SD, %) 23.1 ± 21.5, 3.3 ± 2.9, respectively. Bedding type (manure solids, MS; none, NO; other organic, OR; or sand, SA) were associated with lameness (P = 0.01). Manure solids (lsmeans ± SE; 28.6 ± 1.5) were associated with lower lameness prevalence than SA (33.0 ± 1.4; P < 0.01) and tended to be lower than OR (32.0 ± 1.6; P = 0.06), but not different from NO. There we no differences among NO, OR and SA. The number of rows of stalls (2 row, 2R; 3 row, 3R; or 4 or greater rows, 4R) were associated with lameness prevalence (P = 0.01). There were no differences between 2R (28.5 ± 1.5) or 3R (30.0 ± 1.6), however 4R (38.6 ± 3.5) were associated with increased lameness than 2R (P < 0.01) and 3R (P < 0.01), respectively. Additional factors associated with lameness included hock and knee injury prevalence (P < 0.01, P = 0.02, respectively). Each additional unit increase in hock injury and knee injury prevalence was associated with an increased lameness by 0.2 ± 0.04 and 0.5 ± 0.2, respectively. Each additional hour of pen lying time difference were associated with an increase in lameness prevalence (1.0 ± 0.3; P < 0.01). The findings of this study suggest that by selecting fewer rows per pen and providing certain bedding types can reduce the prevalence of lameness.