Pheromones--chemical signals that can elicit responses in a conspecific--are important in intraspecies communication. Information conveyed by pheromones includes the location of an animal, the presence of food or a threat, sexual attraction, courtship, and dam-pup interactions. These chemical messages remain intact and volatile even when animals, such as rodents, are housed in laboratories rather than their natural environment. Laboratory protocols, such as the cage cleaning and sanitation processes, as well as general housing conditions can alter a rodent's normal production of pheromones in both amount and type and thus may affect behavior. In addition, some procedures induce the release of alarm pheromones that subsequently alter the behavior of other rodents. To prevent pheromonal interference and stress-induced pheromonal release in their research subjects, experimenters should assess current laboratory protocols regarding cage cleaning processes, housing designs, and behavioral assays. Here we discuss how the most commonly used laboratory procedures can alter pheromonal signaling and cause confounding effects.