Purpose The aim of this study is to evaluate the impact of different scatter correction strategies on quantification of high-resolution research tomograph (HRRT) data for three tracers covering a wide range in kinetic profiles. Procedures Healthy subjects received dynamic HRRT scans using either (R)-[11C]verapamil (n = 5), [11C]raclopride (n = 5) or [11C]flumazenil (n = 5). To reduce the effects of patient motion on scatter scaling factors, a margin in the attenuation correction factor (ACF) sinogram was applied prior to 2D or 3D single scatter simulation (SSS). Results Some (R)-[11C]verapamil studies showed prominent artefacts that disappeared with an ACF-margin of 10 mm or more. Use of 3D SSS for (R)-[11C]verapamil showed a statistically significant increase in volume of distribution compared with 2D SSS (p < 0.05), but not for [11C]raclopride and [11C]flumazenil studies (p > 0.05). Conclusions When there is a patient motion-induced mismatch between transmission and emission scans, applying an ACF-margin resulted in more reliable scatter scaling factors but did not change (and/or deteriorate) quantification.