Porcine respiratory coronavirus (PRCV) is a highly prevalent pathogen endemic to many countries, including the UK. It is the causative agent of mild respiratory disease in pigs, however the pathology observed in PRCV infected lung tissue has been reported to compare to that observed in humans infected with severe acute respiratory syndrome related coronavirus (SARS-CoV). SARS-CoV and PRCV infection share common features including prominent lower respiratory tract disease, the disruption of bronchial and alveolar epithelium, lesions, pneumonia and necrosis. These observations have prompted greater interest into the study of PRCV. We have investigated the in vivo phenotype of four strains of PRCV; 86/135308 (135), 86/137004 (137), AR310 (310) and ISU-1. Disparities in both the quantity of infectious viral progeny and PRCV derived RNA were observed in the trachea and lung, with titres of 135 and 137 higher than both ISU-1 and 310. Titres were comparable in nasal swabs, nasal turbinates’, and bronchoalveolar lavage fluid. In vitro replication in ST (porcine swine testis) and LLC-PK1 (porcine kidney) continuous cell lines however did not identify any differences in either productive infection or RNA replication between the four strains. Differential replication was observed in ex vivo tracheal organ cultures (TOCs), providing comparable data to that observed from tracheal samples infected in vivo. These findings have indicated ex vivo TOCs may be a representative alternative to in vivo infection for the study of PRCV in line with the guiding principles of the Three Rs for the replacement, refinement, and reduction of animal resources.