This study investigates the impact of head motion on functional connectivity MRI (fcMRI) estimates. The research involved 1000 healthy young adults, scanned on matched 3T scanners for two resting-state runs. The study found that while most of the variance in fcMRI across subjects was not linked to head motion, head motion had significant, systematic effects on fcMRI network measures. Head motion was associated with decreased functional coupling in the default and frontoparietal control networks, which are characterized by coupling among distributed regions of association cortex. Other network measures increased with motion, including estimates of local functional coupling and coupling between left and right motor regions. Comparisons between groups with subtly different levels of head motion yielded difference maps that could be mistaken for neuronal effects in other contexts. These effects are important to consider when interpreting variation between groups and across individuals. The study also found that head motion is a stable property within subjects, behaving like a trait, and can confound studies exploring individual differences within the same population. The results suggest that head motion significantly affects measures of functional connectivity MRI, with effects depending on the specific measure and including decreased functional coupling for distributed networks and increased functional coupling for local networks. The study highlights the need to carefully consider the effects of head motion on functional connectivity MRI studies that examine individual differences or contrast subject groups. Potential strategies to address head motion include better head immobilization, careful instruction, and advanced methods to regress physiological signals associated with cardiac and respiratory motion. The study concludes that head motion significantly affects measures of functional connectivity MRI even within the range of motion exhibited by typical, healthy young adults. The effects are dependent on the specific measure and include decreased functional coupling for distributed networks and increased functional coupling for local networks. The study emphasizes the importance of considering the influence of head motion in genetic associations, heritability, and relations to behavior and personality.This study investigates the impact of head motion on functional connectivity MRI (fcMRI) estimates. The research involved 1000 healthy young adults, scanned on matched 3T scanners for two resting-state runs. The study found that while most of the variance in fcMRI across subjects was not linked to head motion, head motion had significant, systematic effects on fcMRI network measures. Head motion was associated with decreased functional coupling in the default and frontoparietal control networks, which are characterized by coupling among distributed regions of association cortex. Other network measures increased with motion, including estimates of local functional coupling and coupling between left and right motor regions. Comparisons between groups with subtly different levels of head motion yielded difference maps that could be mistaken for neuronal effects in other contexts. These effects are important to consider when interpreting variation between groups and across individuals. The study also found that head motion is a stable property within subjects, behaving like a trait, and can confound studies exploring individual differences within the same population. The results suggest that head motion significantly affects measures of functional connectivity MRI, with effects depending on the specific measure and including decreased functional coupling for distributed networks and increased functional coupling for local networks. The study highlights the need to carefully consider the effects of head motion on functional connectivity MRI studies that examine individual differences or contrast subject groups. Potential strategies to address head motion include better head immobilization, careful instruction, and advanced methods to regress physiological signals associated with cardiac and respiratory motion. The study concludes that head motion significantly affects measures of functional connectivity MRI even within the range of motion exhibited by typical, healthy young adults. The effects are dependent on the specific measure and include decreased functional coupling for distributed networks and increased functional coupling for local networks. The study emphasizes the importance of considering the influence of head motion in genetic associations, heritability, and relations to behavior and personality.