anomalies) in this study were in line with different studies done in Ethiopia [12, 15, 16, 19]. Advanced maternal age (age greater than or equal to 35 years old) had a significant risk factor for neonatal mortality as identified in this study. This is the fact that advanced maternal age increases the risk that predisposes for different complications for the fetus, and for the neonates as well as for the mother. As indicated in this study, the nonvertex presentation was a determinate factor for neonatal mortality. This was in line with studies done in Southeast Brazil, South Africa, Uganda, and two studies in Ethiopia [12, 13, 16, 24, 25]. The reason for this is that non-vertex presentation is one of the major contributors for prolonged as well as obstructed labour which predisposes the neonate for life-threatening conditions and even for loss of life during the neonatal period. A number of the ANC follow up had significantly reduced the risk of neonatal mortality as point out in this study. This is congruent with studies done in Southeast Brazil, and three studies in Ethiopia [12, 16, 19, 24]. This is obvious that the pregnant mother avoids preventable risk factors after having several ANC follow up, early identification and treatment of pre-existing conditions, and early screening of conditions that occur during pregnancy. In this study, gestational age less than 37 Table 3 Incidence of neonatal mortality among study participants in selected hospitals of Gamo and Gofa Zones, Southern Ethiopia, Neonatal mortality incidence ratio. Fig. 2 Causes of neonatal mortality among study participants in public hospitals of Gamo and Gofa Zones, Southern Ethiopia, 2018/9 (n = 6769) Fig. 3 Timing of neonatal mortality among study participants in public hospitals of Gamo and Gofa Zones, Southern Ethiopia, 2018/9 (n = 6769) Mersha et al. BMC Pediatrics (2019) 19:499 Page 6 of 8 weeks was the determinate factor for neonatal mortality. This was consistent with the study done in Ethiopia [12]. This is because those newborns whose gestation age less than 37 weeks (preterm) are more likely to develop different complications during and after delivery and results for severe morbidity and mortality. Being a male neonate was a significant risk for neonatal mortality as showed in this study. This is in line with some of the studies done in Ethiopia [16, 18, 19]. This is maybe due to the nature that male neonates more risk for different complication as stated in many studies. The public health importance of this study is: Neonates are the risk population group for different complications and most likely affected by preventable causes of morbidity and mortality. Nowadays the neonatal mortality is on the way of decreasing but it is not that much satisfactory as compared to under-five child mortality. So, studies on risk factors that predispose the newborn for ill health and mortality are very important to prevent the underlining causes and to give immediate solutions. The main strength of this study that the design was prospective follow up that it gave a true measure of the incidence of neonatal mortality and to develop cause and effect relationship. Standard and validated verbal autopsy tool was used to measure the causes for neonatal mortality to maintain the validity and reliability. The large sample size was used for this study that resulted in high power and greater precision. The limitations are: response of the verbal autopsy was written based on the respondent’s view and some of the causes were difficult to classify in one category. Besides, during follow up some mothers did not come to health care institutions for immunization as well as for other services and very challenged to trace those mothers as they were out of health facilities. Conclusions This study showed that the incidence of neonatal mortality ratio was optimum. Age of the mother, number of ANC visits, non-vertex presentation, gestational age, and sex of the neonate had significant risk factor neonatal mortality. The major causes of neonatal mortality were prematurity, infection, and birth asphyxia as identified by this study. Both maternal and neonatal risk factors for neonatal mortality were identified in this study. Therefore, early identification of obstetric complications and immediate interventions, strengthen antenatal care services both at the community as well as in the health care institutions, screening the conditions early during intrapartum and postnatal period to give immediate measures to avoid preventable causes of neonatal mortality. The health professionals are responsible to provide quality antenatal care services for pregnant mothers both at health care institutions and in the community. The community is also responsible to seek health information during the prenatal and postnatal period which is provided by health professionals and put in practice. Other scholars should incorporate some of the variables that are not addressed in this study such as wealth index, nutritional status, and cultural aspects. It is also very important if the mixed study design is applied. Supplementary information Supplementary information accompanies this paper at https://doi.org/10. 1186/s12887-019-1881-0. Additional file 1. Tool Additional file 2. STROBE checklist Abbreviations ANC: Antenatal Care; HTN: Hypertension; NICU: Neonatal intensive care unit; NM: Neonatal mortality; VA: Verbal Autopsy Table 4 Bivariate and