Background: Breast cancer (BC) is a complex and heterogeneous diseases, characterized by several molecular subtypes with distinct morphologies and clinical implications that lead to differences in response to various treatment and clinical outcomes. Immunohistochemistry (IHC) is used for molecular subtyping of BC. However, IHC is subject to observer variability. Endpoint RT-PCR gene expression analysis may improve observer variability and diagnostic accuracy. rnObjective: This study aimed to compare IHC with PCR based technology for molecular subtyping of breast cancer. Method and Materials: In this comparative cross-sectional study a total of 54 BC tissue samples were collected from Tikur Anbessa Specialized Hospital (TASH), St. Paul's Hospital Millennium Medical College (SPHMMC), and Yekatit 12 Hospital Medical College. The sample was sent to a Clinic and Polyclinic for Gynecology, Martin-Luther University, Halle Saale, Germany for laboratory analysis. Out of 54 tissue samples, 41 were qualified for IHC analysis of ER, PR, HER2, and Ki-67 protein expression and endpoint RT-PCR analysis of ER, PR, and HER2 gene expression. Kappa statistics were used to assess the concordance between IHC and the endpoint RT-PCR. Furthermore, the socio-demographic and clinico-pathologic characteristics were evaluated. rnResults: The overall percent agreement (OPA) between endpoint RT-PCR and IHC was 68.3% for ER (PPA 71.1%; NPA 33.3%), 39.0% for PR (PPA 14.3%; NPA 92.3%), and 82.9% for HER2 (PPA 62.5%; NPA 87.9%). Cohnâ€™s kappa values of 0.018 (