Vilnius is Lithuania's baroque capital and the obvious first stop, but Kaunas, the country's second city and interwar-era temporary capital, has its own distinct character worth a look.
Vilnius's Old Town (Senamiestis) is a UNESCO World Heritage Site and one of the largest and best-preserved baroque old towns in Eastern Europe, anchored by Gediminas Tower & Upper Castle. Kaunas's Kaunas Castle and Town Hall Square (Rotušės aikštė) are handsome but smaller in scale, reflecting a more modest historic footprint.
Vilnius's Museum of Occupations and Freedom Fights (KGB Museum) is a sobering, essential look at Soviet-era repression, housed in the former KGB headquarters. Kaunas counters with a genuinely eclectic museum scene, including the whimsical Devils' Museum (Žmuidzinavičius Museum) and the harrowing Ninth Fort Museum.
Vilnius mixes baroque churches like St. Anne's Church with a lively, youthful old town scene. Kaunas is known specifically for its interwar Art Deco and Bauhaus-influenced architecture, a UNESCO-recognized style dating from its two decades as Lithuania's provisional capital between the world wars — a look Vilnius doesn't have.
Vilnius is the larger, more visited capital with more flights, hotels, and nightlife. Kaunas is under an hour and a half away by train or bus, making it an easy day trip or overnight add-on rather than a competing destination.
Choose Vilnius for the region's best-preserved baroque old town and Lithuania's main museums and nightlife. Choose Kaunas for a distinct interwar architectural style and a quirkier, less touristy museum scene. They're close enough (about 90 minutes apart) that combining both on one Lithuania trip is easy and common.