San Marino 0-1 Lithuania Donatas Kazlauskas scored and was sent off as the visitors cemented top spot in Group 1 and condemned San Marino to a third straight defeat.
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Lithuania won 1-0 against San Marino to continue their fine start to qualifying for the 2015 UEFA European Under-21 Championship.
Lithuania had picked up a win and a draw from their opening two fixtures en route to the Czech Republic, and are now top of Group 1 by three points thanks to a goal from half-time substitute Donatas Kazlauskas three minutes after the interval. Though the same player was dismissed late on, Lithuania held on to condemn their hosts to a third successive defeat.
Lithuania take on Finland, currently second in the section, on 5 September, with San Marino entertaining Wales the following day.
"We didn’t play a great match, but we got the three points which is the most important thing," said Lithuania coach Arminas Narbekovas. "We deserved the victory because we created a lot of opportunities to score."
San Marino coach Pierangelo Manzaroli added: "We played a great match. We played well defensively in the first half, we were up against it but not conceding many great opportunities. However, it is disappointing because the winner came from our mistake."