Background and aims: There are established rules of perioperative antibiotic prophylaxis in adults. In neonates there are no precisely described such rules. In this group of patients this problem is additionally complicated by the risk of intrauterine infection and immature immunity. Aims: To compare two guidelines of perioperative antibiotic prophylaxis in neonates: only for 3 days and up to the moment when negative CRP is obtained. Methods: In randomised controlled trial betweein 1st of June 2012 and 30th of June 2013 we assesed the group of 44 term neonates with congenital malformations who required surgery after birth. In 16 neonates perioperative antibiotic prophylaxis was started on the 1 day before surgery and was continued for 3 days regardless of the level of CRP on a day 3. In 28 neonates perioperative antibiotics prophylaxis was also started on the day 1 before surgery and was continued up to the moment when negative CRP was obtained. The endpoint was the observation of the patients after surgery regarding possible episodes of the secondary infection. Results: In a group of neonates who have received antibiotics for 3 days as a perioperative prophylaxis we observed no secondary infection. In a group of neonates who received antibiotics as a perioperative prophylaxis up to the negative CRP was obtained we observed 17 secondary infections. This difference was statistically significant. Conclusions: Long-lasting perioperative antibiotic prophylaxis in neonates did not protect against secondary infection in term neonates withon 30 days after surgery. Precise guideline for perioperative antibiotic prophylaxis in neonates requires further investigation.