Using museum materials and recently trapped specimens of field voles (Microtus agrestis (Linnaeus, 1761)) from Lithuania and Estonia, we assessed temporal and latitudinal trends in body and skull size, comparing the periods 1980–1996 and 2014–2016. We measured four body and 23 skull characters, size-adjusting them using the geometric mean procedure. A pronounced decrease in the size of M. agrestis was noted in Estonia, where 23 out of 27 adjusted body and skull characters had decreased by up to 21.9%, with only the tail length, hind foot length, maximum height of mandibula excluding coronoid process and coronoid height of mandibula increasing significantly. Decreases were less marked in voles from Lithuania – most pronounced were a 6.1% decrease in adjusted body length, an 11.6% decrease in adjusted length of the braincase, a 3.85% decrease in the breadth of the braincase, measured at the widest part, a 2.9% decrease in condylobasal skull length and a 2.2% decrease in the height of the braincase. The coronoid height of the mandibula of Lithuanian individuals showed an 8.4% size increase. In both countries, the confounding effect of sex on the size changes of M. agrestis from 1980 to 2016 was much smaller than the effect of time period. Concluding, voles in Estonia became significantly smaller, while changes in the measured characters in Lithuania were heterogeneous.