We hypothesize that use of postoperative heparin deep vein thrombosis prophylaxis influences development of surgical site infection (SSI) after colorectal surgery. From July 2008 to June 2009, patients undergoing an abdominal operation by colorectal surgeons at a single university-affiliated teaching hospital were prospectively followed and more than 80 variables collected. One hundred eighty-one patients were identified. Forty-five per cent (n = 82) received heparin prophylaxis and 55 per cent (n = 99) did not. SSI occurred in 23 per cent (n = 19) of patients receiving heparin versus 9 per cent (n = 9) who did not (P = 0.02). Univariate analysis found SSI to be associated with heparin (P = 0.02) and increased operative time (P = 0.03). Multivariate analysis showed that SSI was associated only with heparin use (P = 0.04; OR, 2.6; 95% CI, 1.1 to 6.6).