Pygopagus comprises 17% of all conjoined twin cases. Survival rate is higher compared to other variations of conjoined twins, but separation is a great challenge due to multiorgan involvement. Intraoperative neuromonitoring (IONM) used aims to aid operator in preserving as much function as possible.The authors reported 2 pairs of pygopagus separation. Intraoperatively, motor-evoked potential (MEP) and sensory-evoked potential (SEP) were used in all patients. Three patients survived in which all had transient motor deficits. Urinary retention was reported in one patient. One patient died 2 weeks after separation as twins only had one kidney which was spared for the healthier twin.IONM was used to guide operator in dissecting, identify the ownership of the neural structures, and determine the safest point to separate in pygopagus separation. Despite the normal MEP and SEP recordings, transient motor weakness may still occur transiently. The motor tract development of children is achieved in adolescence, making MEP less accurate. However, the reliability of MEP increases when it is combined with SEP. Autonomic function monitoring such as bulbocavernosus reflex (BCR) could not be assessed due to the unavailability of the probe.IONM can aid operator in pygopagus separation during determining the origins of the structure, dissecting, and cutting the neural structures. Normal MEP interpretations are still possible to correlate with transient deficits, but reliability can be improved with the use of SEP. In surgeries involving the lower spine level, BCR monitoring is recommended to avoid autonomic deficits.