A method is provided for managing animals (10) in a milking system which comprises a milking stall (11) provided with a milking apparatus (13) for milking the animals, a gate arrangement (18a-b; 18a-b, 32; 55a-b) allowing the animals to enter said milking stall, one at a time, from at least two different locations, and a control device (15) which holds and updates a milking suitability index for each of the animals. According to the method a first animal is identified and received at a first location, and a milking suitability index for the first animal is retrieved. A second animal is identified and received at a second location, and a milking suitability index for the second animal is retrieved. The milking suitability indexes for the first and second animals are compared and an animal at either one of said first and second locations is allowed to enter the milking stall depending on the outcome of the comparison.