In the wars which ravaged the Estonian countryside for two generations (1558–1629), the indigenous population and the continuity of settlement suffered most. About 250 000–300 000 people had lived on Estonian territory before the Livonian War; in the 1620s their number was 120 000–140 000. By the early 17th century about three quarters of the farms were deserted; the areas surrounding the large cities and on the Polish–Swedish border were devastated; the least ravaged was Ösel (Saaremaa). However, Ösel (Saaremaa) was raided by both the Swedes (the Nordic Seven Years’ War, 1566, 1568) and the Russians (1576). The wars were accompanied by infectious diseases (the plague in the early 17th century, during the Swedish–Polish war), with a number of victims comparable to the number of war casualties. In addition, Estonia suffered from the failure of crops which had affected the whole of northern and eastern Europe, and the famine which accompanied it. The population was restored only after the unification of the whole country under Swedish rule. By 1695, the Estonian population was estimated at 400 000 (cf. Finland, ca 450 000; Latvia, ca 800 000).

The 17th century can be characterised by internal migration: the indigenous people moved from densely populated areas of Estonia to less populated ones. A large number resettled on the mainland from Saaremaa, which had been spared due to its isolation from the rest of Estonia. Settlers from Russia came to East and South Estonia, and from Finland — partly encouraged by the Swedish authorities — to North and Mid-Estonia. In the mid-17th century, Finns constituted 20% of the population in North-East Estonia (Viru County) and 12% in North Estonia (Harju County). The proportion of non-Estonian population in the 1620s was estimated at a little less than one fifth. The immigrants were assimilated quickly; except for the Old Believers who, having fled Russia after the religious reforms, settled on Lake Peipus: they remained a distinctive ethnic group. Russians who had settled on the Estonian–Latvian border under the Polish reign constituted the core of the town of Valga. On the south-western and western islands there were Swedish villages, the result of immigration in the Middle Ages.

The steady growth of the Estonian population continued until the outbreak of the plague in 1657 and the Great Famine (1695–1697), which started as a result of unfavourable climatic conditions in the successive summers. In the hardest years at the end of the century, about a fifth of Estonian population perished (70 000–75 000 people); the situation was hopeless, as the Famine also struck in Sweden (ca 80 000–100 000 dead) and in Finland (one quarter died), less so in Latvia and north-west Russia.

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