Objective To compare perinatal and maternal morbidity associated with caesarean sections performed in the first with that performed in the second stages of labour. Patients and methods Comparative analyses between nulliparous women with singleton term pregnancies who had a caesarean section in the first stage of labour and those who had a second stage caesarean section were completed using standard statistical methods. A subgroup analysis, according to indication for caesarean section, was also performed. Results Of 627 women, 81% had caesarean delivery in the first stage and 19% had caesarean delivery in the second stage of labour. Women undergoing caesarean delivery at full cervical dilatation were 1.9 times more likely to have an augmented labour (95% CI 1.2-3.4, P < 0.001) and 2.8 times more likely to have epidural anaesthesia in labour (95% CI 1.5-5.2, P < 0.001) than those in the first stage. Compared with caesarean delivery in the first stage of labour, women undergoing caesarean delivery at full cervical dilatation were 4.6 times more likely to have composite intraoperative complications (95% CI 2.7-7.9, P < 0.001), 3.1 times more likely to have blood loss greater than 1,000 ml (95% CI 1.3-7.4, P = 0.01), and 2.9 times more likely to have a blood transfusion (95% CI 1.5-5.6, P < 0.001). The risk of neonatal morbidity was higher in first stage caesareans when they were performed for presumed fetal compromise (66.3 vs. 26.3%, P = 0.002), and lower when they were performed for failure to progress (18.4 vs. 42%, P = 0.02). Conclusion Caesarean section in the second stage of labour is associated with a higher risk of maternal but not perinatal morbidity.