The purposes of this study were to examine the effect of sensitivity encoding (SENSE) factors on cortical thickness measurements and to determine which SENSE factor to use to reliably measure cortical thickness in 3.0 T and 1.5 T T1-weighted MRI images. The 3D T1-TFE images were acquired from 11 healthy volunteers with 6 different SENSE acceleration factors from 1.0 (without SENSE acceleration) to 4.0 on a 1.5 T scanner, and 9 different SENSE factors from 1.0 to 6.0, plus a second-day 1.0 acquisition on a 3.0 T scanner. Cortical thickness was calculated for the entire cortical surface that was further subdivided into 33 regions. Repeated measures multivariate analysis of variance revealed that the main effect of SENSE factors (F=12.485, df=7, p=0.006) was a significant underestimation of cortical thickness at SENSE 5.0 (p=0.022) and 6.0 (p=0.011) at 3.0 T and at SENSE 4.0 (p<0.000) at 1.5 T. Repeated measures ANOVA showed that thickness measurements at the insula, superior temporal sulcus, the medial part of the superior frontal lobe, and cingulate cortex are highly affected by SENSE factors. SENSE factors affect thickness estimation more significantly at 1.5 T and thus 1.5 T imaging provides less reliable estimates using SENSE techniques. Faster imaging can be done without too much loss of reliability using a high SENSE factor, such as 3.0, at 3.0 T with acquisition time being inversely proportional to the SENSE factor.