Cultured myometrial (M) and fibroid (F) smooth muscle cells (SMCs) have been widely used as a model for the study of F growth. The aim of this study was to compare gene expression profiles using microarrays between six paired M and F tissues from hysterectomy specimens, as well as cells isolated from the same tissues and cultured for up to three passages. A total of 2055 genes were differentially expressed by ANOVA between all experimental groups. Among them, 128 genes were found to be statistically different between M and F tissues. More than 1100 genes were significantly changed between tissues and cultured cells, with 648 genes common between both M and F cells at P0 and P3. Expression profiles of six genes including estrogen receptor-α (ERα) and progesterone receptor (PR) were also validated using real-time PCR. These data demonstrate that large changes occur in SMC gene expression in culture, reducing differences between M and F cells. They also show that ERα and PR levels are reduced in cells compared with whole tissue. These results indicate that although M and F cell cultures provide an important tool to study these tumours, in vitro studies must be carefully planned and evaluated to provide meaningful results.