Housing systems are an important element in the well-being of laboratory animals and, consequently, influence the outcomes of animal experiments. Individually ventilated cage (IVC) systems were developed to maintain low ammonia and CO(2) concentrations, to support a low relative humidity, and to reduce spread of infective agents and allergenic contaminants. However, the increased intracage ventilation rates (25 to 100 air changes/h) in these systems have animal welfare implications. In four preference studies involving a total of 36 pairs of female BALB/c mice and three different types of IVC racks, we tested the preference/avoidance of mice for the intracage ventilation rate, cage size, location of air supply, and presence of nesting material in a two-cage system. In this system, the two cages were connected by a passage with a swing-door to allow mice to move freely between the cages. We found that the mice avoided high intracage ventilation rates but that providing nesting material could counteract this avoidance. In addition, the mice preferred larger cages and an air supply in the cover. We conclude that the location of the air supply in the cage, cage size, ventilation rate and the presence of nesting material in IVC systems influence the well-being of the animals.