Having Inter professional perspective is very important in healthcare programs. Healthcare team members face different challenges in complex systems such as neonatal intensive care unit (NICU). Inter professional collaboration is a way of dealing with challenges in the process of practicing and improving the care. The aim of this study is to explore the challenges of inter professional collaboration which can be observed by the healthcare providers in the neonatal intensive care unit in Isfahan. This was a focused ethnographic study conducted in two neonatal intensive care units in Isfahan (Shahid Beheshti and Al-Zahra hospitals). The data was collected through a 14-month period from November 2012 to January 2014. Observations and interviews were used for data collection and content analysis was used to explore the data. Three main challenges were found in this study from the data analysis. They were: “organization challenges’’, ‘environment challenges ’’ and ‘‘being honest in crisis’’. This study investigates the challenges of inter professional collaboration among healthcare providers in NICUs in Iran. In this study an ethnographic approach focused on healthcare provider's interactions in every day was used in the NICU environment. The results of this study can help us to create new inter professional collaboration cultures in different wards of hospitals particularly NICUs.