Digital dermatitis (DD) is an infectious disease of the digital skin of dairy cows that is associated with compromised animal welfare and significant economic losses. The hind feet of 16,098 dairy cows from 55 herds were examined in the milking parlor, and DD lesions identified were classified using the M-score system and swabbed for PCR testing. Swabs were also collected from hind feet with normal digital skin for comparison. Data on farm construction and lameness prevention measures were collected through direct observation and in-person interviews with farm managers. Herd-level risk factors for DD were investigated using mixed-effects logistic regression models, with Farm ID included as a random-effects variable. The average within-herd and herd prevalence of DD were 6.4 % (95 % CI: 4.9–8.0 %) and 92.7 % (n = 51, 95 % CI: 85.9–99.6 %), respectively. Among the investigated DD lesions, DD-associated treponemes were identified at frequencies of 87 % for Treponema spp., 87.5 % for T. medium, 86.2 % for T. phagedenis-like, and 78.3 % for T. pedis. Additionally, Fusobacterium necrophorum and Dichelobacter nodosus were identified at frequencies of 37 % and 15.4 %, respectively. Samples from normal digital skin exhibited substantially lower frequencies for all bacterial species investigated. Risk factors significantly associated with DD in the final multivariable model included practice of preventive early lactation trimming (OR=0.45, 95 % CI: 0.26–0.78) and the presence of an abrasive bedding on farms (OR=1.6, 95 % CI: 1.01–2.6). This comprehensive molecular and epidemiological analysis enhances under­standing of DD etiology in Egypt and contributes to the development of effective control programs to improve cow welfare and support the sustainability of milk production.