The Invisible (Seeing and Not Seeing in Vilnius) by Laimonas Briedis (2008) — A layered meditation on Vilnius as a palimpsest city, exploring how different occupiers and communities have seen and erased each other. The best single book for understanding why Vilnius looks and feels the way it does.
Between Shades of Gray by Ruta Sepetys (2011) — A young adult novel following a Lithuanian girl deported to Siberia in 1941. More gripping than its genre usually manages, and historically accurate. Gives the Soviet deportations a human face that academic histories struggle to provide.
The Gates of Dawn by Czesław Miłosz (1955) — A semi-autobiographical novel by the Polish Nobel laureate, who grew up in the Vilnius region and whose relationship with the city was complicated and lifelong. Miłosz wrote extensively about Vilnius and its different peoples; this novel is the most accessible entry point.
Vilna on the Seine by Yitskhok Rudashevski (published posthumously) — A diary kept by a 14-year-old Jewish boy in the Vilna Ghetto between 1941 and 1943. Rudashevski was killed at Ponary. The diary survived. It is one of the most important documents of the Holocaust in Lithuania.