Objective: To describe the incidence of ankylosing spondylitis (AS) and spondyloarthritis (SpA) in the Danish population in 2000–2013, at national and regional level, and to investigate any trends in incidence over time. Methods: From the Danish National Patient Registry (NPR), we identified patients diagnosed with AS (International Classification of Diseases, 10th revision: M45) or SpA (M46) from 1 January 2000 to 31 December 2013. Patients without a relevant contact in NPR at 12–24 months after initial diagnosis were excluded. Incidence rate ratios (IRRs) were calculated using the background population of men and women aged 18–45 years in 2000–2013 as a comparator. Variations in incidence between periods and the five Danish regions were evaluated. Results: In total, 3042 incident cases were identified (AS: 1849; SpA: 1193). AS incidence increased from 476 in 2000–2004 to 660 in 2010–2013; the IRR (95% confidence interval) increased from 1.49 (1.33–1.67) in 2005–2009 to 1.74 (1.53–1.97) in 2010–2013. SpA incidence increased from 156 in 2000–2004 to 707 in 2010–2013; the IRR increased from 2.45 (2.03–2.94) in 2005–2009 to 6.31 (5.27–7.55) in 2010–2013. The incidence of both AS and SpA increased in all five regions. Conclusion: The incidence of both AS and SpA in Denmark increased from 2000 to 2013. However, the proportion of patients diagnosed with SpA rather than AS was significantly higher in 2010–2013. This may be due to increased awareness of SpA and new treatment options, but possibly also misclassification of patients with SpA.