Dystocia, defined as difficult or abnormal parturition where assistance is required, is common in dogs and often lead to acute Caesarean section. The incidence of dystocia is high foremost in small and giant breeds. When performing Caesarean section anaesthetics, the physiological changes that the bitch undergoes during pregnancy and transplacental transfer of anaesthetics to the neonates must be considered. Few comparative studies on anaesthetic regimens for canine Caesarean section have been published. Analgesia is normally provided pre- and post-operatively when surgery is required. However, limited research is available on how analgesics, transferred to the neonates via the placenta and milk, affect the neonates. Analgesia is therefore often limited during and after Caesarean section in the bitch for fear of complications. The routine at the University Animal Hospital (UDS), Swedish University of Agricultural Sciences (SLU), Uppsala, is usually to administer one dose of opioids intraoperatively after the neonates have been removed from the uterus during surgery. This retrospective study was performed on journals from 95 caesarean sections performed at UDS, SLU, Uppsala from the 15th of November 2010 to the 28th of May 2013, and also the study period complemented with follow-up telephone interviews with 70 of the dog owners. The effect of opioid administration on neonatal mortality was also studied by comparing the results of the present study with the results from a previous study also performed at UDS, SLU, where the same anaesthetic regimen was used for Caesarian section but no analgesia was administered to any of the 141 bitches. No difference in neonatal mortality could be observed up to eight weeks of age between bitches that were given analgesia compared with those that were not given any analgesia. In bitches weighing 10 kg or less, the risk of neonate death up to the age of eight weeks was 4.8 times higher than the risk for neonates born by bitches weighing more than 10 kg.