
Varėna District Municipality is a municipality in Alytus County in southern Lithuania.

Čebatoriai is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 114 people.

The Čepkeliai Marsh is the largest bog in Lithuania. Located in Varėna District Municipality, south of Marcinkonys village and north of Kotra River, which flows along the Belarus–Lithuania border in this area.
Česukai is a village in Varėna district municipality, in Alytus County, southeastern Lithuania. According to the 2001 census, the village has a population of 5 people. The village is located 1 km south to Merkinė, between Nemunas and Merkys rivers, at Dzūkija National Park. Česukai is surrounded by a pine forest and it is only reachable by a forest road which branches from Vilnius-Hrodno highway.

Dainava Forest also the Druskininkai-Varėna Forest, historically the Hrodna Forest, or the Gudian Forest is the largest forest in Lithuania. Located in Dzūkija region in southern Lithuania, it covers the total area of 1,450 km2 (560 sq mi) of which 1,290 km2 (500 sq mi) is covered by trees. A large part of the forest is protected by the Dzūkija National Park and the Čepkeliai Nature Reserve.
Darželiai (Varėna) is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 61 people.
Daržinėlės is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 12 people.

Dubininkas is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 5 people.

Giraitė is a village in Matuizų eldership, Varėna district municipality, Alytus County, southeastern Lithuania. According to the 2011 Census, the population was 61, down from 89 at the 2001 census.

Glūkas is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 4 people.
Grybaulia is a small village in Dzūkija National Park in Lithuania. The village is best known for its extensive fish ponds, which, surrounded by boreal forests provide breeding, feeding and wintering habitats for a number of bird species.
Ilgininkai is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 161 people.
Kabeliai is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2011 census, the village has a population of 168 people.
Kapiniškiai is an ethnographic village in Lithuania. It is located in the Dzūkija National Park south-west of Marcinkonys. According to the 2001 census, it had 54 residents.

Kašėtos (Marcinkonys) is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 24 people.

Kašėtų gyvenvietės is an archaeological site in Varėna district municipality, in Alytus County, in southeastern Lithuania.

Kibyšiai is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 212 people.
Kijučiai is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 166 people.

Kirklionys is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 3 people.
Kriviliai is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 421 people.
Krūminiai is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 207 people.
Kurmiškė (Varėna) is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 10 people.
Liškiava is a historic village in the Varėna district municipality, Lithuania. It is situated on the bank of Nemunas River, near the Lake Liškiavis. In 2005 its population was 37.

Mančiagirė is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 24 people.
Marcinkonys is a village in Varėna district, Lithuania, located south-east of Merkinė. It is the administrative center of the Dzūkija National Park and Čepkeliai Marsh. According to the 2020 estimate, it had 591 residents.

Mardasavas (Marcinkonys) is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2011 census, the village has a population of 26 people.
Margionys is a village in Dzukija National Park in Lithuania, located south-west of Marcinkonys. It is located 115 km away from Vilnius, 50 km away from Alytus and at the hand's reach from Druskininkai.
Masališkės is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 88 people.
Matuizos is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2011 census, the village has a population of 1201 people.
Mergežeris is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2011 census, the village has a population of 30 people.

Merkinė is a town in the Dzūkija National Park in Lithuania, located at the confluence of the Merkys, Stangė, and Nemunas rivers. Merkinė is one of the oldest settlements in Lithuania. The first settlers inhabited the confluence of Merkys and Nemunas in the 9th-10th century BC, at the end of the Paleolithic. On top of Merkinė hill-fort stood one of the most important Lithuanian castles, built in the 13th century, which guarded against invasions of the Teutonic Order. Merkinė was a part of a strategic triangle - Kaunas - Vilnius - Merkinė, protected with the chains of hillforts and castles. The center of Merkinė town is a state-protected urbanistic monument. Merkinė is an important point of Lithuania's domestic tourism.
Musteika is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2011 census, the village has a population of 61 people.

Nedzingė is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 288 people.
Noruliai is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 47 people.
Pagilšys is a village in Varėna District Municipality, in Alytus County, in southeastern Lithuania.The village had a population of 11 people according to the 2001 census and 6 people according to the 2011 census.
Palkabalis is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 22 people.

Pamerkiai is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 131 people.

Pamusiai is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 74 people.

Puvočiai is a village in Marcinkonių eldership, Varėna district municipality, Alytus County, southeastern Lithuania. According to the 2001 census, the village had a population of 71 people. At the 2011 census, the population was 57.

Roduka is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 34 people.

Rūsingė is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 31 people.
Samūniškės is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 41 people.

Šarkiškės is a village in Varėna district municipality, in Alytus County, southeastern Lithuania. According to the 2001 census, the village has a population of 48 people.
Senovė (Varėna) is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 10 people.
Šklėriai is a village in Varėna district municipality, in Alytus County, southeastern Lithuania. According to the 2001 census, the village has a population of 74 people.
Subartonys is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village had a population of 75 people.

Trasninkas is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 11 people.
Valkininkai is a historic town in Valkininkų (Valkininkai) eldership, Varėna district municipality, Alytus County, Lithuania, located about 22 km (14 mi) northeast from Varėna and about 55 km (34 mi) southwest from Vilnius. At the 2001 census its population was 238 and at the 2011 census it was 229.

Vilkiautinis is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 353 people.
Vydeniai is a village in Varėna district municipality, in Alytus County, in southeastern Lithuania. According to the 2001 census, the village has a population of 413 people.

Žeimiai is a village in Varėna district municipality, in Alytus County, southeastern Lithuania. According to the 2001 census, the village has a population of 70 people. It is situated on the left bank of the Neman River in Dzūkija National Park.
Zervynos is an ethnographic village in the Varėna district, Lithuania. It is situated within the territory of the Dzūkija National Park near the Ūla River. The Saint Petersburg–Warsaw Railway runs through this village. Zervynos has 48 homesteads; 8 homesteads and 32 separate buildings are officially declared ethnographic monuments. The village was among the sites short-listed for nomination for the UNESCO World Heritage Site. Though the village is isolated by the Dainava Forest, it is a busy place during summer as tourists kayaking in the Ūla River pass through the settlement.

Žiūrai is a village in Varėna district municipality, in Alytus County, southeastern Lithuania. It is situated on Ūla River. According to the 2001 census, the village has a population of 35 people.