Objective: Head motion is one of the most common sources of artefacts in brain MRI. When imaging young children, general anaesthesia is common, which is a limited resource. We evaluate the performance of markerless prospective motion correction (PMC) and selective reacquisition in a complete clinical protocol for brain MRI, comparing acquisitions with and without instructed intentional head motion.Materials and Methods: Image quality metrics and ratings were analysed for scans with and without PMC - acquired with six 2D- and 3D-encoded sequences in twenty-two healthy adults. The influence of PMC on motion-artefact-related changes in cortical thickness estimates was quantified using a general linear model.Results: For the motion-degraded 3D-encoded MPR and FLAIR sequences, image quality increased with PMC and reacquisition (p<0.001, corrected). Motionless scans with PMC showed slightly reduced (p < 0.05, corrected), but still diagnostic image quality. Cortical thickness estimates were widely correlated with motion level in the uncorrected scans (p<0.05), which was not apparent to the same extent in PMC scans. For the motion-degraded 2D-encoded TSE, STIR and DWI sequences we observed higher image quality with PMC and reacquisition (p<0.001, corrected), though the effect size varied. We did not observe an improvement in the T2* sequence (p>0.05, corrected), which is known to be sensitive to motion-related changes in B0. Discussion: Using PMC and selective reacquisition in sequences for standard clinical brain MRI improves diagnostic image quality when there is head motion.