Purpose To analyze the relationship between intraoperative cultures and the development of surgical site infection (SSI) in women undergoing laparotomy for gynecological surgery. Methods Prospective observational cohort study. Over a six-year period, women who underwent elective laparotomy at our hospital were included. Patients’ demographics, underlying co-morbidities, surgical variables, type and etiology of postoperative surgical site infections were collected. Skin and subcutaneous samples were taken just prior to skin closure and processed for microbiological analysis. Univariate and multivariate analyses (logistic regression model) were conducted to explore the association of the studied variables with SSIs. Results 284 patients were included in our study, of which 20 (7%) developed surgical site infection, including 11 (55%) superficial and nine (45%) organ-space. At univariate analysis, length of surgery, colon resection, transfusion and positive intraoperative culture were associated with surgical site infection occurrence. Skin and subcutaneous cultures were positive in 25 (8.8%) and 20 (7%) patients, respectively. SSI occurred in 35% of women with positive subcutaneous culture and in 20% of those with positive skin cultures. Using multivariate analysis, the only independent factor associated with surgical site infection was a positive subcutaneous culture (OR 10.4; 95% CI 3.5–30.4; P<0.001). Conclusion Intraoperative subcutaneous cultures before skin closure may help early prediction of surgical site infection in open gynecological procedures.