critical window of opportunity for the prevention and management of maternal and newborn complications, which can otherwise prove fatal. A large “proportion of” newborn illnesses and deaths can also be prevented using simple, low-cost interventions during delivery and the week following partum [9]. Reducing neonatal mortality is increasingly important not only because deaths that occur during the neonatal period is increasing as under-five mortality declines but also health interventions needed to address the major causes of neonatal deaths generally differ from those needed to address other under-five deaths [10]. A significant proportion of these neonatal deaths could be prevented by the appropriate management of the neonate presenting complications, such as very low birth weight, < 30 gestational weeks at birth or an Apgar score at the 5th minute of life < 7 [11]. Analysis of different studies in Ethiopia showed that the incidence of the neonatal mortality rate was ranged from 17.2 to 35.5 per 1000 live births [12–17]. The most determinate factors which were identified by previous studies were birth order, frequency of antenatal care, delivery place, twin delivery and size of neonate [12, 18, 19]. Birth asphyxia, neonatal infections, and prematurity were the three leading causes of neonatal mortality [12, 13]. Newborns in Ethiopia gaining attention through the Global Maternal Child Survival Program: Contributes to reductions of neonatal morbidity and mortality through capacity-building in high-impact services both at the community and the primary health care unit levels. The activity supports the government of Ethiopia to improve community maternal and newborn health practices and care-seeking behaviors; increases the provision of quality community-based newborn care services including management of newborn sepsis, and strengthens the supportive systems with a focus of district capacity building [20]. This program is underway, but to scale up a comprehensive way of implementation identifying determinate factors intensively is very important to reduce neonatal mortality further. Different studies were conducted in assessing determinates for neonatal mortality but there is a need to assess the immediate postnatal (within 2 days following delivery) cause of neonatal mortality that the majority of deaths occurred at that time. Therefore, there is a need for research in public hospitals of Gamo and Gofa Zones to assess the incidence, underlying causes and determinate factors for neonatal mortality. Methods Study setting, period and design This prospective follow up study was conducted in public hospitals of Gamo and Gofa Zones from April 5, 2018, to March 5, 2019. There are six hospitals in Gamo and Gofa Zones but this study was done in selected three public hospitals (Arba Minch General Hospital (AMGH), Sawla General Hospital (SGH) and Chencha Primary Hospital (CPH)). The total population of the study area is 2,019, 687. The estimated number of women of reproductive age (15–49) is 470,587 from this, the estimated number of delivery is 69,881 and the estimated number of live birth is 69,881. In Gamo and Gofa Zone, the institutional skilled delivery rate is 51.2% [21, 22]. Sample size determination Epi info7 software Stat Cal was used to estimate the sample size for this study. The assumptions used were prevalence of neonatal mortality among unexposed group (gestational age greater than 37 weeks) was 2.9% (p1 = 0.029) and the prevalence of neonatal mortality among exposed group (gestational age less than 37 weeks) was 5.8 (p2 = 0.058) from the study conducted in Southwest Ethiopia [12], 95% level of confidence, power of 90, and the ratio of 1:1. So, the calculated sample for this study was 2433 after adding a non-response rate of 10%. But, the sample size used for this study was 6769 Mersha et al. BMC Pediatrics (2019) 19:499 Page 2 of 8 based on the number of live births in the respective hospitals in 1 year period. Data collection tool A structured interviewer-administered pre-tested questionnaire and standard abstraction checklist to review data from medical records were used to collect the data. The tools were developed adapted by reviewing different works of literature. A standard verbal autopsy (VA) questionnaire was used to collect the data on causes of neonatal death. The tool was developed and validated by WHO, Johns Hopkins University (JHU) and the London School of Hygiene and Tropical Medicine [23] (Additional files 1 and 2). Data collection procedures A well-trained six BSc holder midwives prospectively identified neonates who experienced mortality cases during the follow-up period. As this was a prospective follow-up study; data were collected in different phases: In the first phase: all the baseline information in the hospital was collected either by interviewing or by abstracted from medical records. The data were collected from the delivery ward, postnatal ward and neonatal intensive care unit (NICU) of each hospital. For the neonates that died in the hospital stay, VA was conducted at a point in time, and case notes were used to collect the information. But, for those neonates who survived in the hospital stay the second phase proceeded at the end of the neonatal period. So, newborns were assessed for mortality cases whether they died within 28 days of life or survived and for those who don’t