Neonatal period is a susceptible time in which the newborn has to adapt to a totally new environment and is vulnerable to many problems, which may even be life threatening. Analyzing the neonatal disease pattern helps health care givers and policy makers to design better strategies. This study aimed to assess the pattern of diseases and associated factors among neonates admitted to neonatal intensive care unit at Jimma university medical center, Jimma, Southwest Ethiopia Retrospective cross-sectional study design was conducted from March 15 to 30, 2018 among neonates admitted over a period of two years (January 1, 2016 to December 31, 2017) on 341 samples. Systematic random sampling technique was employed to get required samples from database. Data was entered to Epi-data 3.1 and exported to SPSS Version 23 for analysis. Bivariate and multivariate logistic regression was used to analyze the association between dependent and independent variables and P-value <0.05 at 95% CI was declared statistically significant association. The main disease patterns identified were neonatal sepsis (19.9%), prematurity (14.0%) and hyaline membrane disease (11.9%). More than half (55.56%) of neonates were admitted in the first 24 hours. Neonatal sepsis, prematurity, and hyaline membrane disease were the most frequently occurring diseases.