**Background:** Severe feather pecking (SFP) and cannibalism (CA) are serious welfare, performance, and economic problems in commercial laying hen flocks, particularly in alternative housing systems. The provision of manipulable litter is considered an important preventive measure, but evidence-based information from systematic longitudinal studies on the association between litter condition and plumage damage (PD) and skin lesions (SL) has been lacking. This study aimed to investigate the effects of litter condition on the occurrence of PD and SL in commercial layer farms using a longitudinal design.
**Methods:** Twenty-eight laying hen flocks (9 white egg-laying, 19 brown egg-laying) on 11 farms in Saxony, Germany, were studied from May 2019 to September 2021. Hens were housed in barns with aviaries (n=21) or free-range systems (n=7; nonorganic, 4 m² free-range area per hen) with a median flock size of 12,357 hens (1st–3rd quartile: 5,671–16,996). Pullets were housed at 17.4 ± 0.8 weeks of life. Integument scoring (PD and SL) was performed 7 times (laying months 0, 1, 2, 3, 5, 7, 9, 11) on 50 randomly selected hens per flock per time point, using Welfare Quality® guidelines (3-point scales for plumage and skin lesions; total plumage score calculated by summing 3 body region scores). Litter condition was assessed 12 times via visual scoring (litter quality, cake formation, structure, litter height) and chemical analysis (dry matter, nitrogen, phosphorus, pH) of pooled samples from 3 barn locations. Intraobserver reliability was very good (PABAK values: 0.90–0.94). Binary logistic regression models with farm as random effect were used, with age, hybrid type, and housing system forced into models as known risk factors.
**Key Results:** Over the entire laying period, mean litter height was 6.84 ± 2.10 cm, dry matter content was 70.87 ± 9.86%, nitrogen content was 2.48 ± 0.48%, phosphorus content was 0.84 ± 0.19%, and pH was 6.99 ± 0.59. The litter total score (LTS) showed significant associations with both PD and SL (both P < 0.001). In the final models, PD and SL increased with age (P < 0.001). White egg-laying flocks had lower PD than brown egg-layers (OR 0.44, 95% CI 0.33–0.58, P < 0.001). Free-range housing was associated with lower PD (OR 1.76, 95% CI 1.67–1.83, P < 0.001) and lower SL (OR 1.57, 95% CI 1.34–1.83, P < 0.001) compared to barn housing. For litter traits: increasing litter height was associated with lower PD (OR 0.97, 95% CI 0.97–0.99, P < 0.001) and lower SL (OR 0.99, 95% CI 0.98–0.99, P < 0.001). Cake formation was associated with higher PD (OR 1.71, 95% CI 1.57–1.89, P < 0.001) but not SL (P = 0.369). Poorer litter structure was associated with higher PD (OR 1.11, 95% CI 1.01–1.21, P = 0.025) but not SL (P = 0.216). Higher dry matter content was associated with lower PD (OR 0.99, 95% CI 0.98–1.00, P = 0.022) and lower SL (OR 0.99, 95% CI 0.99–1.00, P < 0.001). Higher phosphorus content was associated with lower PD (OR 0.87, 95% CI 0.80–0.95, P = 0.002) and lower SL (OR 0.84, 95% CI 0.77–0.91, P < 0.001). Higher nitrogen content was associated with increased SL (OR 1.03, 95% CI 1.01–1.06, P = 0.007) but not PD (P = 0.608). Litter quality and pH showed no significant associations. No differences in feed nutrient contents were found between LC+ and LC− flocks.
**Clinical Implications:** This study provides strong evidence that litter condition is a significant risk factor for plumage damage and skin lesions in commercial laying hen flocks. Specifically, caked, poorly structured, flat, and moist litter increases the risk of behavioral disorders, while deeper, drier, well-structured litter with higher phosphorus content is protective. These findings support practical recommendations for egg producers to monitor and maintain high-quality litter as a key management strategy. The current practical recommendation of litter height under 4 cm may need reconsideration given the protective effects of greater litter height observed in this study. Further research is needed to clarify the pathophysiological mechanisms linking litter nitrogen and phosphorus content to behavioral disorders.