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Background  More than five million perinatal deaths occur each year globally. Despite efforts put forward during the millennium development goals era, perinatal deaths continue to increase relative to under-five deaths, especially in low- and middle-income countries. This study aimed to determine predictors of perinatal death in the presence of missing data using birth registry data from Kilimanjaro Christian Medical Center (KCMC), between 2000–2015.    Methods  This was a retrospective cohort study from the medical birth registry at KCMC referral hospital located in Moshi Municipality, Kilimanjaro region, northern Tanzania. Data were analyzed using Stata version 15.1. Multiple imputation by fully conditional specification (FCS) was used to impute missing values. Generalized estimating equations (GEE) were used to determine the marginal effects of covariates on perinatal death using a log link mean model with robust standard errors. An exchangeable correlation structure was used to account for the dependence of observations within mothers.    Results  Among 50,487 deliveries recorded in the KCMC medical birth registry between 2000–2015, 4.2% (95%CI 4.0%, 4.3%) ended in perinatal death (equivalent to a perinatal mortality rate (PMR) of 41.6 (95%CI 39.9, 43.3) deaths per 1,000 births). After the imputation of missing values, the proportion of perinatal death remained relatively the same. The risk of perinatal death was significantly higher among deliveries from mothers who resided in rural compared to urban areas (RR = 1.241, 95%CI 1.137, 1.355), with primary education level (RR = 1.201, 95%CI 1.083, 1.332) compared to higher education level, with <4 compared to ≥4 antenatal care (ANC) visits (RR = 1.250, 95%CI 1.146, 1.365), with postpartum hemorrhage (PPH) (RR = 2.638, 95%CI 1.997, 3.486), abruption placenta (RR = 4.218, 95%CI 3.438, 5.175), delivered a low birth weight baby (LBW) (RR = 4.210, 95%CI 3.788, 4.679), male child (RR = 1.090, 95%CI 1.007, 1.181), and were referred for delivery (RR = 2.108, 95%CI 1.919, 2.317). On the other hand, deliveries from mothers who experienced premature rupture of the membranes (PROM) (RR = 0.411, 95%CI 0.283, 0.598) and delivered through cesarean section (CS) (RR = 0.662, 95%CI 0.604, 0.724) had a lower risk of perinatal death.    Conclusions  Perinatal mortality in this cohort is higher than the national estimate. Higher risk of perinatal death was associated with low maternal education level, rural residence, <4 ANC visits, PPH, abruption placenta, LBW delivery, child’s sex, and being referred for delivery. Ignoring missing values in the analysis of adverse pregnancy outcomes produces biased covariate coefficients and standard errors. Close clinical follow-up of women at high risk of experiencing perinatal death, particularly during ANC visits and delivery, is of high importance to increase perinatal survival.

Predictors of perinatal death in the presence of missing data: A birth registry-based study in northern Tanzania