Abdominal wall defects are serious birth defects, with long periods of hospitalization and significant costs to the medical system. Nosocomial infection (NI) may be an additional risk factor that aggravates the evolution of newborns with such malformations. Methods: in order to analyze the factors that may lead to the occurrence of NI, we performed a retrospective study over a period of thirty-two years (1990–2021), in a tertiary children’s hospital; 302 neonates with omphalocele and gastroschisis were eligible for the study. Results: a total of 33.7 % patients were infected with one or more of species of bacteria or fungi. These species were Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter spp., Staphylococcus spp., Enterococcus spp. or Candida spp., but the rate of NI showed a significant decrease between the 1990–2010 and 2011–2021 period (p = 0.04). The increase in the number of surgeries was associated with the increase in the number of NI both for omphalocele and gastroschisis; in the case of gastroschisis, the age of over 6 h at the time of surgery increased the risk of infection (p = 0.052, marginal statistical significance). Additionally, for gastroschisis, the risk of NI was 4.56 times higher in the presence of anemia (p < 0.01) and 2.17 times higher for the patients developing acute renal failure (p = 0.02), and a hospitalization period longer than 14 days was found to increase the risk of NI 3.46-fold (p < 0.01); more than 4 days of TPN was found to increase the NI risk 2.37-fold (p = 0.015). Using a logistic regression model for patients with omphalocele, we found an increased risk of NI for those in blood group 0 (OR = 3.8, p = 0.02), in patients with a length of hospitalization (LH) of ≥14 days (OR = 6.7, p < 0.01) and in the presence of anemia (OR = 2.5, p = 0.04); all three independent variables in our model contributed 38.7% to the risk of NI. Conclusion: although in the past 32 years we have seen transformational improvements in the outcome of abdominal wall defects, there are still many factors that require special attention for corrections.