The aim was to assess the results of primary anastomosis (PA) compared to enterostomy (ES) in infants with spontaneous intestinal perforation (SIP) and a weight below 1000 g. Between 2014 and 2016, enterostomy was routinely carried out on extremely low birth weight (ELBW) patients with SIP. From 2016 until 2019, all patients underwent anastomosis without stoma formation. We compared outcome and complications in both groups. Forty-two patients with a median gestational age of 24.3 weeks and a birth weight of 640 g with SIP were included. Thirty patients underwent PA; ES was performed in 12 patients. Overall in-hospital mortality was 11.9% (PA: 13.3%, ES: 8.3%). Reoperations due to complications became necessary in 10/30 patients with PA and 4/12 patients with ES. Length of stay was 110.5 days in the PA group and 124 days in the ES group. Median weight at discharge was higher in the PA group (PA: 2258 g, ES: 1880 g, p = .036).Conclusion: Primary anastomosis is a feasible treatment option for SIP in infants < 1000 g and may have a positive impact on weight gain and length of hospitalization. However, further studies on selection criteria for PA are necessary. What is Known:• Enterostomy (ES) and primary anastomosis (PA) are feasible treatment options in preterm infants with spontaneous intestinal perforation (SIP).• Stomal complications or failure to thrive due to poor food utilization can pose significant problems. What is New:• Primary anastomosis in case of SIP is equal to enterostomy in terms of mortality and revision rate; however, length of stay and weight gain can be presumably positively influenced.• Primary anastomosis is a valid treatment option even for patients weighing less than 1000 g.