male neonates. Of the neonates, 65 (1.0%) encountered birth trauma during delivery. From those 24 (36.9%) of the neonates had cephalhematoma, 9 (13.8%) developed caput succedaneum and 32 (49.3%) had others (fracture, bruising and subgleal hemorrhage) (Table 2). Incidence of neonatal mortality In this study inter and intra-hospital neonatal mortality incidence ratio was estimated with a 95% level of confidence per 1000 live births. The highest proportion of neonatal mortality was reported from Chencha Primary Hospital that 1.0% (95%CI: 0.5, 2.20%) Overall, neonatal mortality incidence ratio in selected three public hospitals was 0.96% (95%CI: 0.75, 1.22%) (Table 3). Causes and timing of neonatal mortality In this study, 65 neonatal deaths occurred during the follow-up period in selected three public hospitals of Gamo and Gofa Zones, Southern Ethiopia. Of the neonatal deaths, only 52 respondents were agreed and interviewed for verbal autopsies but rest were refused for verbal autopsy. Almost half (51.9%) of the neonatal deaths were happened due to prematurity or gestational age less than 37 week, 13 (25%) due to neonatal infection, 7 (13.5%) were by birth Fig. 1 Overall process of the study conducted in public hospitals of Gamo and Gofa Zones, Southern Ethiopia, 2018/9 Mersha et al. BMC Pediatrics (2019) 19:499 Page 4 of 8 asphyxia, 3(5.8%) congenital malformation due congenital malformation and the rest were with unspecified cause (Fig. 2). Regarding the timing of neonatal deaths, 24 (46.2%) died within 24 h, and 2 (3.8%) died after the day 8 up to 28 days (Fig. 3). Determinates of neonatal mortality After adjusting in the multivariable model age of the mother, the number of ANC visits, presentation, gestational age at birth, and sex of the neonate were significantly associated with neonatal mortality. Advanced maternal age above 35 years old increased neonatal mortality significantly as compared to the age group 15 to 24 years old (β =1.34; 95% CI:0.54,2.14). The antenatal care visit of four or more significantly reduced neonatal mortality as compared to those who have no visit (β = − 0.88; 95% CI:-1.54,-0.21). Non-vertex presentation (β = 1.15; 95% CI: 0.59, 1.69), gestational age of less than 37 week (β =1.18; 95% CI: 0.46, 1.89), and being male neonate (β =0.91; 95% CI: 0.21, 1.61) had significantly increased neonatal mortality (Table 4). Table 1 Socio-demographic and economic characteristics of study participants in public hospitals of Gamo and Gofa Zones, Southern Ethiopia, 2018/9 (n = 6769) Characteristics Frequency Percentage Age 15–24 3002 44.3 25–34 3384 50.0 ≥ 35 383 5.7 Marital status Married 6430 95.0 Othera 339 5.0 Ethnicity Gamo 3725 55.0 Gofa 1519 22.4 Otherb 1525 22.6 Educational status of the father No formal education 1026 15.2 Primary (1–8) 1636 24.2 Secondary (9–12) 2027 29.9 College and above 2080 30.7 Occupation of the father Farmer 1773 26.2 Merchant 2497 36.9 Government employer 1974 29.2 Wavier 275 4.1 Daily laborer 250 3.7 The average income per month < 70.8USD 1775 26.2 70.8-177USD 3195 47.2 > 177USD 1799 26.6 a single, divorced and separated due to work b Zayise, Amhara, Oromo, Gurage, Woliata, Konso, Derashe, Oyida, and Gidicho. Table 2 Maternal and child health and obstetric factors of study participants in public hospitals of Gamo and Gofa Zones, Southern Ethiopia, 2018/9 (n = 6769) Variables Frequency Percentage Number of ANC visit No visit 765 11.3 1–3 1820 26.9 ≥ 4 4184 61.8 Hemorrhage Yes 315 4.7 No 6454 95.3 Cause of hemorrhage Placenta praevia 108 34.3 PPH 153 48.6 Othera 54 17.1 Prelabour rupture of membrane Yes 1262 18.6 No 5507 81.4 Hypertension during pregnancy Yes 524 7.7 No 6245 92.3 Classification of HTN Pre-eclampsia 297 56.7 Eclampsia 74 14.1 Chronic hypertension 77 14.7 Gestational hypertension 76 14.5 Presentation Vertex 5818 86.0 Non-vertexb 951 14.0 Sex of the neonates Male 3606 53.3 Female 3163 46.7 Gestational age < 37 week 808 11.9 ≥ 37 week 5961 88.1 Birth weight < 2500 g 600 8.9 ≥ 2500 g 6169 91.1 Baby referred to other health facilities Yes 77 1.1 No 6692 98.9 a accreta/increta/percreta, hemorrhage during delivery, uterine rupture, and other obstetric hemorrhages, and b breech, transverse, face, and brow. Mersha et al. BMC Pediatrics (2019) 19:499 Page 5 of 8 Discussion In this study neonatal mortality incidence ratio were 9.6(95%CI: 7.5, 12.2) per 1000 live births. Age of the mother, number of ANC visit, non-vertex presentation, gestational age, and sex of the neonate had significant risk factor for neonatal mortality. The major causes of neonatal mortality were prematurity, infection, and birth asphyxia. The incidence of neonatal mortality was lower than studies done in northern Ethiopia (18.6 per 1000 live births), Kersa Health and Demographic Surveillance system site in Ethiopia (27.5 per 1000 live births) and two studies in southwest Ethiopia (35.5 and 27 per 1000 live births). But, it was higher than one study done in South Central Ethiopia (4.8 per 1000 live births) [12, 14–17]. The reason for this is the study period difference along with advance in the health care system that people’s attitudes and awareness about conditions that put the newborn for ill health and increase in health-seeking behavior from time to time. The causes of neonatal mortality (prematurity, infection, birth asphyxia, and