An experiment was carried out with 128 Ross chicks to evaluate the effects of Salmonella Enteritidis phage type 4 inoculated in eggs (contamination site vs inoculum), observing the site of inoculation by injection in allantoidal cavity or by shell direct contact and the combination with presence or absence of Salmonella Enteritidis phage type 4. Chicks were distributed in a completely randomised 2x2 factorial design (contamination site and inoculum). We evaluated the frequency of infected chicks, the morphology of the small intestinal mucosa from day 1 to 21 of age, and its performance. Salmonella Enteritidis phage type 4 inoculated in allantoidal cavity showed high frequency of intestinal colonisation at hatch, but reduced with age. The histomorphometrical evaluation indicated reduction in villus height (P<0.05) and increase in crypt depth in duodenum and ileum at day 1. At day 21, villus height was similar to the control, and crypt depth was deeper (P<0.05). The lowest performance (P<0.05) was observed at days 14 and 21 and highest feed conversion at day 14. The fast-growth lineage showed increased jejunum crypt depth (P<0.05). At day 21, no difference was found in the intestinal mucosa parameters or in weight gain and feed conversion in chicks inoculated with Salmonella Enteritidis in the albumen. Changes were evident in the histomorphometric parameters, which resulted in lower weight gain at days 14 and 21.