There is some controversy over whether the extraction of upper second permanent molars as part of orthodontic treatment leads to the over eruption of unopposed lower second permanent molars. A study was established to investigate the presence of any over-eruption in a group of subjects who had upper second permanent molars extracted as part of a previous course of orthodontic treatment. These subjects (the experimental group) were compared with a control group of subjects, matched for age and sex. Upper and lower impressions were taken, and the vertical positions of the posterior teeth were objectively assessed from the study models using the travelling microscope. Measurements from the study models showed that the distal aspect of the lower second permanent molar had over erupted in the experimental group when compared to the control (P <0·001 right, P<0·05 left). The degree of over-eruption was influenced on the mesial aspect by the distal position of the upper first permanent molar (P<0·01), but the distal aspect was not. Eruption of the upper third molar did not affect the over-eruption of the lower second permanent molar in the experimental group. The majority of upper third molars had erupted at least 3 years since the upper second molars had been extracted, but the majority had erupted into an unfavourable contact position with the Just permanent molar.