PURPOSE This study aimed to determine differences in neutrophil levels between those receiving long-course neoadjuvant chemoradiotherapy (nCXRT) and those proceeding straight to surgery (StS) for rectal cancer, and in those who developed serious septic events within 30 post-operative days within each group. METHOD Patients undergoing elective surgery between 2006 and 2008 were retrospective reviewed. Some 38 received nCXRT, and 46 proceeded StS. Statistical techniques included repeated measures analyses. RESULTS There was no significant difference in serious 30-day septic rates (anastomotic leaks, pelvic abscess or generalised sepsis) between treatment groups (nCXRT, 11%; StS, 13%; p = 1.000). Neutrophil levels in the nCXRT group fell significantly and remained lower throughout treatment than those proceeding StS (p <0.001 within groups, p <0.001 between groups). The difference in means of the treatment groups was different for those with sepsis than for those without, and the difference in means of those with sepsis and those without is very different for the two treatment groups (p = 0.018). CONCLUSION Chemoradiotherapy reduced neutrophil levels throughout treatment, and post-operative septic patients in this group had even lower levels. Further studies are warranted to fully assess the relationship of neutrophil levels to sepsis, using standardised definitions of sepsis.