There is a worldwide development toward using data from hospital-based stroke registers to estimate epidemiological trends. However, incomplete case ascertainment may cause selection bias. We examined the completeness of case ascertainment and selection bias in two hospital-based Swedish stroke registers. First-ever stroke cases between March 2015 and February 2016 in the catchment area of Skåne University Hospital, Lund, Sweden, were included from multiple overlapping sources: two hospital-based stroke registers, Riksstroke-Lund and Lund Stroke Register (LSR); local outpatient and inpatient registers; primary care registers; and autopsy registers. The resulting population-based cohort was used as reference to assess completeness of case ascertainment and patient characteristics in Riksstroke-Lund and LSR. In total, 400 stroke patients were identified. Riksstroke-Lund detected 328 (82%) patients, whereas LSR detected 363 (91%). Patients undetected by hospital-based registers had higher 28-day case fatality than those detected (44% vs 9%; P=.001). Patients only detected in primary care (n=11) more often lived in healthcare facilities compared with those detected by hospital-based registers (57% vs 7%; P=.001). Patients not detected by Riksstroke-Lund, but detected by population-based sources, had less severe strokes (median NIHSS 3 vs 5; P=.013). Some first-ever stroke patients, such as those with high early case fatality and those with mild stroke, may go undetected with hospital-based screening used in clinical stroke registers. This can result in selection bias due to not identifying specific groups of patients including some with high early case fatality and those living in healthcare facilities.