Aukštaitija National Park was established to protect:

• The upper reaches of the Žeimena River ecosystem at the confluence of three unique landscape zones, the Ažvinčiai (Gervėčiai) Old Forest and Baltis Lake natural complexes, the Baluošas, Linkmenas-Ūkojas, Tauragnas and Utenas bowl-shaped valleys with their many lakes and forests, the Šiliniškės mid-lake ridge and the Ladakalnis, Benediktavas (Makiai) moraine massif and the Kiauna valley landscape, the Petriškė geomorphological and Būka, Juodupė, Švogina, Pliaušė, Labažė, Asalnai and Žeimena hydrographical complexes, the Kretuonas, Kretuonykštis, Knytis and Pažeimena biotic communties, as well as other rare and disappearing plants and animals, and other natural territorial complexes and objects.
• The remains of 12th – 15th century north east Lithuanian defensive lines including the Taurapilis, Ginučiai, Puziniškis, Linkmenas, Vajuonis and other castle mounds, the Rėkučiai ancient defensive embankments, the unique Kretuonas archeological complex, the Minčia, Vyžai, Šakarva, Palūšė, Kaltanėnai, Šventa and other barrows and Stone Age settlements, the ethnographically valuable Salos (II), Varniškės (II), Vaišnoriškės, Šuminai (Pabaluošė), Strazdai (Šariškė), Kretuonys, Benediktavas and other villages also rich in ethnographical elements, the Kaltanėnai urban complex, the Palūšė church architectural ensemble, water mills within the park territory, the Stripeikiai bee-keeping museum, and other cultural heritage values;
• The stability of the source of the Žeimena River natural ecosystem, the biota components and their diversity.

The Aukštaitija National Park is situated in the territory between the Baltic upland strip lake complexes and the northern Nalšia (Švenčionys) upland strip hills. The structure of the national park is one of the most complex ones compared to other state parks. The park is characterised by the exclusiveness and abundance of the natural and cultural heritage sites, and especially large recreational and educational tourist as well as ethno-cultural potential. Aukštaitija National Park is classified under the top category from the perspective of the exceptional value of the landscape.

The major landscape types found in the park: forested hilly glacial-type lakes (tunnel valley systems), groups of small lakes, laky swampy waterholes, shallow forested terraced valleys, forested glacio-fluvial terraces, forested undulating elevations, forested morainic hilly massifs and ridges, and agrarian morainic hilly massifs.

These are the territories of European Community importance (code, title) found in the park: 3140 Hard oligo-mesotrophic waters with benthic vegetation, 3150 Natural eutrophic lakes with Magnopotamion or Hydrocharition – type vegetation, 3160 Natural dystrophic lakes and ponds, 6410 Molinia meadows on calcareous, peaty or clayeysilt-laden soils (Molinion caeruleae), 7110 Active raised bogs, 7140 Transition mires and quaking bogs, 7160 Fennoscandian mineral-rich springs and springfens, 7210 Calcareous fens with Cladium mariscus and species of the Caricion davallianae, 7230 Alkaline fens, 9010 Western Taïga, 9050 Fennoscandian herb-rich forests with Picea abies, 9080 Fennoscandian deciduous swamp woods, 91D0 Bog woodland.

The total number of plant species is 992, of these 96 are included in Lithuania’s Red Data Book. The total number of animal species is 2, 961. Mammals – 54, of these 18 are protected by the European Community, and 14 are included into the Lithuania’s Red Data Book. Birds – 243, of these 68 are protected by the European Community, and 70 are included into the Lithuania’s Red Data Book. Fishes – 41, of these 3 are included into the Lithuania’s Red Data Book. Amphibians and reptiles – 17, of these 8 are protected by the European Community, and 4 are included into the Lithuania’s Red Data Book. Invertebrates – 2,606, of these 14 are protected by the European Community, and 39 are included into the Lithuania’s Red Data Book.

The following zones have been established in the Aukštaitija National Park to protect its natural and cultural heritage values: 2 strict nature reserves and 28 reserves (7 landscape, 1 geomorphological, 7 hydrographical, 4 botanical-zoological, 5 telmological, 2 cultural, and 1 urban).

The strict nature reserves in the national park have been established to protect the following: the Ažvinčiai (Gervėčiai) ancient woods – the typical example of an East Lithuanian ancient woods with communities typical of this region; rare plant and animal species; Baltys – the typical thermokarst lake waterhole with the hydrological and biocenose complex of a high scientific value; rare plant and animal species and the remains of the ancient woods.

The landscape reserves have been established to protect: Baluošas – an especially picturesque thermokarst lake and forests‘ landscape complex characteristic to the Aukštaitija region with the unique Baluošas Lake; the ethnographic lake-side villages, and rare hydrographical and biotic elements; Benediktavas – an especially distinctive complex of Aukštaitija‘s hilly forested agrarian landscape; the richly planted Benediktavas village of high ethnographic value; and the archeological values; Kiauna – the natural hydrographic structure of the Kiauna River mid-section with the river-side villages of Stirninė, Vasiuliškės and Žvirbliškės typical to Aukstaitija‘s region; Kretuonas – the unique natural and cultural complex of high ecological importance with the archaeological findings of the national importance and ethnographically valuable village of Kretuonys; Šiliniškės – one of the most distinctive complexes of lake-rich tunnel valleys in Lithuania; the unique inter-lake Šiliniškiai ridge, Ginučiai oak forest, other natural and archeological values; Tauragnas – the picturesque tunnel valley of the deepest in Lithuania Tauragnas Lake; the unique valley of Tauragna Stream which dries off seasonally, the geomorphologically valuable Šeimatis morenic complex; the structures of the Taurapilis and Daunoriai agrarian landscape typical of the Aukštaitija hill massif; one of the best known in the country Taurapilis archeological complex; and other values of the natural and cultural heritage; Utenas – the natural complex of a large tunnel valley complex with many lakes and forests typical to the Aukstaitija‘s region, with an abundance of archeological and biotic values.

The Petriškė Geomorphological Reserve has been established to protect the unique Petriškė erosional plateau.

The hydrographical reserves have been established to protect: Asalnai – the Asalnai and Dringykščai Lakes, the bays and lakeshore areas at the southwestern end of Dringis Lake; especially beautiful hydrographical complex of bays and junction canals, and the rare plant and animal habitats found around the lakeshore; Būka – the unique structure of the Būka River bed with the typical river biotic communities; Juodupė – the complex of a natural forest stream Juodupė and the wetlands of its upper reaches; Labažė – the Labažė lakelet and the natural Labažė Stream that flows out of it and the forested sub-valley with the biocenoses typical of such small valleys; Pliaušė – the natural complex of the Pliaušė Stream and small lakes with the growing sites of rare plant species and Black Grouse breeding grounds; Švogina – the beautiful structure of the Švogina River, its forested valley with natural grasslands and rare plant species; Žeimenys – the structure one of the most distinctive tunnel valley intersections in Lithuania with islands and peninsulas and wintering areas of rare bird species.

The botanical-zoological reserves have been established to protect: Ažvinčiai Forest – the biocenoses typical to the Aukstaititja‘s region with the habitats of rare and semi-rare plant and animal species; Minčiagirė – the Minčia Stream forest biocenoses with the habitats of rare plant and animal species; Knyčia – the national park’s largest raised bog; the natural Knyčia stream and its surroundings with rare plant and animal species; Žeimena – the scenic Žeimena River valley, habitats of rare plant and animal species in the river, its flooded grasslands and sub-valley forests.

The telmological reserves have been established to protect: Kriogžlys – forested inter-lake wetland, typical of eastern Lithuania, that is known for its rare flora, the Capercaille and other rare bird species, with the eutrophic Kriogžlys Lake; Kretuonykštis – one of the largest lake swamp complexes in eastern Lithuania that is of great ornithological value, also featuring archeological artifacts; Pagilūtė – the Pagilūtis swamplands, as the most complex wetland ecosystem in the national park, distinguished for its rare plant species and its ornithological value; Siūriai – the unique forested, swampy lakeshore and riverbank complex, a typical example of a natural swampy stream and the particularly distinctive structure of the Dringis lakeside; Vilkaraistis – one of the largest lakeshore mire complexes in eastern Lithuania with habitats of rare plant and animal species.

The cultural reserves have been established to protect: Salos – the typical Aukštaitija region lakeshore village; Varniškės – the typical Aukštaitija region forest village.

The Rėkučiai Archaeological Reserve protects one of the largest historical defensive embankments in Lithuania, and the Rėkučiai and Paversmis barrow archaeological complex.

The Kaltanėnai Urban Reserve was established to protect the historical development of the Kaltanėnai town planning and spatial structure with its central rectangular-shaped town-square, the manor site, as well as other architectural and memorial values.

There are 16 state protected natural heritage objects in the Aukštaitija National Park. The most important of them are the following natural monuments: Ladakalnis, Baluošas Lake island, Dringis horn, the Goat horns, the stones Mokas and Mokiukas, the lakelets (the blue and green eyes of the godess Laumė), the Asalnai Pine Tree, the Labakaršis Pine Tree. The national park contains 150 cultural heritage objects, 20 of these are cultural monuments.