Animals that are seized for cruelty or neglect may face prolonged stays at shelters while investigations are ongoing. With the support of American Humane, this study assessed the behavior and welfare of animals housed in animal shelters or animal control facilities as a result of cruelty or neglect. Data were collected from a local shelter with a large annual intake (over 20,000 dogs and cats per year). The shelter’s classifications in the cruelty and neglect category include abandonment, severe emaciation, abuse or torture, or lack of food, water or shelter. Cats were housed from 1 to 105 days. Dogs were housed from 1 to 57 days. Over 40% of the animals sheltered for cruelty or neglect were subsequently euthanized. Further study to identify the needs of this unique subpopulation of animals is warranted to identify appropriate interventions and management guidelines to enhance their health and welfare at the facility, which could in turn improve adoptability and overall outcome.