Most studies of dental microevolution have used the standard methodologies employed in dental anthropology: buccolingual/mesiodistal lengths and the frequencies of non-metric dental traits. In this work we use the occlusal polygon method which is based on a polygon created by linking the four molar cusp apices using digital analysis. This method has been used to identify different evolutionary trends in Neandertal and modern humans; our objective was to assess the existence of changes in the occlusal polygon area, and thus the general morphology of first upper molars, between two Portuguese samples from the Late Neolithic (4130 +/- 90 BP) and the early 20th century. This method allows us to evaluate both tooth size and relative cusp position in the occlusal plane. Contrary to the accentuated tooth size reduction commonly found from the past 10000 years using buccolingual/mesiodistal measurements, no statistically significant change of the total occlusal area of the crown was observed between these samples. Nevertheless, we report an increase of 7.45% in the size of the occlusal polygon and hence 9.38% in its relative area, from 27.30% of the total crown area to 30.30% over this time span. This result implies that microevolutionary changes among Portuguese populations led to changes in the positions of the cusps relative to one another in the first upper molar, whereas the location of their apices have moved away from the centre of the crown to a more peripheral position. This apparent increasing trend contrasts with the one reported in studies of both Neandertals and modern humans.