Aviary systems for laying hens offer space and opportunities to perform natural behaviors. However, hen welfare can be impaired due to increased risk for keel bone and foot pad disorders in those systems. This cross-sectional study (N = 47 flocks) aimed to assess prevalences of keel bone and foot pad disorders in laying hens housed in aviaries in Belgium to identify risk factors for these disorders and their relation to egg production. Information on housing characteristics and egg production were obtained through questionnaire-based interviews, farm records, and measurements in the henhouse. Keel bone (wounds, hematomas, fractures, deviations) and foot pad disorders (dermatitis, hyperkeratosis) were assessed in 50 randomly selected 60-week-old laying hens per flock. A linear model with stepwise selection procedure was used to investigate associations between risk factors, production parameters, and the keel bone and foot pad disorders. The flock mean prevalences were: hematomas 41.2%, wounds 17.6%, fractures 82.5%, deviations 58.9%, hyperkeratosis 42.0%, dermatitis 27.6%, and bumble foot 1.2%. Identified risk factors for keel bone disorders were aviary type (row vs. portal), tier flooring material (wire mesh vs. plastic slats), corridor width, nest box perch, and hybrid. Identified risk factors for foot pad disorders were aviary type (row vs. portal), free-range, and hybrid. Percentage of second-quality eggs was negatively associated with keel bone deviations (P = 0.029) at the flock level. Keel bone and foot pad disorders were alarmingly high in aviary housing. The identification of various risk factors suggests improvements to aviary systems may lead to better welfare of laying hens.