This Bernardine monastary and church date back to 1468 when a wooden church was built here. In 1471, they started to build the brick version, which completed by sometime around 1503. In 1812 when Napoleon's army came through, they used the church for storing flour. The last major renovation happened in 1936 but then during the Soviet occupation it was again turned into a warehouse (for medical equipment, apparently) and ended up suffering major interior damage. In between it suffered several fires, wars, and various alterations and reconstructions, but it's still standing.
When we were there in July 2009, it was just starting to undergo some major renovations. It was open to the public, filled with temporary seating, and already being used for masses. The catacombs under the altar are all exposed, and much of the artwork and architectural details are still intact, although damaged. I could have easily spent many hours in there with a camera and tripod, but alas, I only ended up getting a few quick snapshots.
Further reading (Google-translated Lithuanian websites):