Elephants experience a number of health issues that can contribute to their well-being and survival. In managed populations, housing conditions and management practices can influence individual health, so potential risk factors associated with morbidity or mortality should be identified to ensure the best possible standards of care. The goal of this study was to determine if the number of clinical events experienced could be a useful welfare indicator in zoo elephants, and to determine factors associated with key pathologies. We used an epidemiological approach to investigate how intrinsic (species, sex, age) and extrinsic (housing, management) factors were associated with both the total number of clinical events, and each of the four most prevalent pathology types (gastrointestinal issues, skin lesions, lameness, foot lesions), over a 12-month period. The study included 220 (127 African; 93 Asian) elephants housed at 61 facilities across North America. More than 1100 clinical events were identified. Species and sex differences were apparent in the types of pathology encountered, and unsurprisingly, the number of clinical events was positively correlated with age. Factors relating to housing (percent time with indoor/outdoor choice, space experience inside, number of unique environments an elephant was housed in, percent time on soft substrate) and management (enrichment diversity, spread of feeding opportunities) were also related to the number of clinical events. However, relationships were often counter to our initial hypotheses, highlighting caution in assuming cause and effect from correlational analyses such as these. Other welfare indicators such as serum and fecal glucocorticoids and serum prolactin were also associated with health status, being higher or more variable in individuals with a greater number of events. This approach provides insight into housing and management factors related to the health of these species in zoos, and in some cases, may reflect management changes that have already been made to mitigate existing or anticipated health concerns.