Juninho scored the only goal of the match as Middlesbrough secured a slight advantage in this first leg of the Carling Cup semi-final.
The Brazilian fired a low shot into the Arsenal goal just after half time. It came after he had hit the post just 15 minutes into the match at Highbury.
A youthful Gunners side piled on the pressure in the second half, but they failed to find the net.
It was their first domestic defeat in 30 games this season.
Arsenal's Ray Parlour (left) and Boro's Juninho
Arsne Wenger fielded an experimental side, combining seasoned players like Martin Keown and Ray Parlour with rising stars like David Bentley.
Vital
Ugo Ehiogu produced a towering display in defence for Boro, making some vital interceptions late on.
Boro missed a couple of good chances in the dying seconds of the game, which they may come to regret in the return leg at The Riverside in a week's time.
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