Introduction The Cancer Patient Pathway for Non-specific Symptoms and Signs of Cancer (NSSC-CPP) has been implemented in Denmark with regional and intra-regional differences. In some places, the initial diagnostic work-up (often including a CT scan) is performed by general practitioners (GPs) and in others by hospitals. Variations may influence the use of Organ Specific Cancer Patient Pathways (OS-CPPs) and prognostic outcomes for the patients. Therefore, the aims were: 1) To analyse how a CT scan referred from GP or hospital is followed by OS-CPPs and NSSC-CPPs at the national and regional level, and 2) To analyse, nationally and regionally, the diagnostic outcomes of persons referred to CT scan by either GP or hospital six months after and mortality one year after CT scan. Methods A nationwide population-based study including individuals with a first CT scan in 2013-2016, either referred from GP or hospital. Results Overall, individuals with a CT scan referred from GPs were more likely to start a NSSC-CPP or an OS-CPP than individuals with a CT scan referred by hospitals. Across the five Regions in Denmark, CT scans referred by GPs were associated with reduced odds of total mortality in all regions; (North, OR=0.78 [0.73 0.83], Central, OR=0.92 [0.87 0.96], South, OR=0.85 [0.81 0.89], Capital, OR=0.96 [0.91 1.00] and Zealand, OR=0.85 [0.79 0.90]) and increased odds of cancer-specific mortality in four regions, ORs ranging from 1.15-1.51 with no difference in Region North (1.00 [0.91 1.10]). Conclusion No obvious association between more CT scans and CPPs and reduced diagnoses and mortality was observed. The different diagnostic models might not explain the prognostic outcomes, but the different use of CT scans in, and between Regions play a large role in the differences in incidence and mortality.