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 (