One of the main causes of allergic reactions in young animals is β-conglycinin, an antigenic glycoprotein found in soya beans. Therefore, the objective of the study was to investigate the effects of a prior immunisation with β-conglycinin on growth performance, serum immunoglobulin levels and intestinal histology in piglets. Forty piglets (7 d of age) were randomly divided into four groups of ten piglets each. Piglets of Groups Im and Im+S were immunised twice by hypodermic injection with β-conglycinin at 500 μg/kg body weight (BW) at day 7 and 21 of age. At day 23, Groups Im+S and S were intramuscularly injected with 5000 μg β-conglycinin per kg BW. The piglets of Group C received a physiological saline solution by hypodermic injection. All piglets were weaned at the age of 23 d and blood samples were taken on days 7, 21 and 35. At the end of the trial, five piglets per group were slaughtered and the intestine was collected for evaluating mucosal histology. Compared to Group C, in Group S the average daily gain (ADG), feed intake and gain:feed ratio were decreased (p < 0.01), and serum levels of IgG and IgE were increased (p < 0.01). Furthermore, in this group the structure of duodenal and jejunal mucosa was severely damaged. But in Groups Im and Im+S the ADG was increased (p < 0.05), serum IgE levels were decreased (p < 0.01) and the intestinal mucosa was not damaged. The results suggest that prior immunisation with β-conglycinin can increase ADG and serum IgG levels and decrease serum IgE levels. Therefore, this method is also potentially able to protect the structural integrity of the intestinal mucosal epithelia and alleviate allergic reactions in piglets.