Animals such as pigs which are to be slaughtered at slaughterhouses are unloaded from the transport truck and driven into pens and stalled in these for some time, until they are driven out of the pens and over to a stunning apparatus. The pigs of a supplied lot to the slaughterhouse, or part of the supplied lot, are treated as a separate unit during one or more of the above-mentioned stages of treatment, which means that pigs of a unit are to be constantly kept separated from pigs belonging to other units. Each unit may comprise e.g. 15 pigs. The treatment of the animals in units reduces their aggressions, and their well-being is increased, which will result in a lower incidence of rind damages, blood splashings and deviant meat quality of the carcasses. A system for stalling of the pigs includes a number of oblong pens (1), which are placed next to each other. Each of the pens has an entrance gate (6), an exit gate (8) and a driving gate (10) which is movable in the longitudinal direction of the pen. Each pen is equipped with one or more stationary intermediate gates (4), which are placed at such a distance from each other, the entrance gate (6) and the exit gate (8), that the pen is divided into several rooms (3a, 3b, 3c). The size of each room corresponds preferably to the size of the unit of pigs which is to be treated.