For much of this season it has seemed as ridiculous to question Chelsea's defensive capabilities as to wonder whether Jose Mourinho might go several weeks without being embroiled in a controversy. But as Mourinho celebrated his team's passage to the semi-final from his hotel room last night, his delight may have been tempered by concern at the state of his backline.

Conceding three times to Bayern here hardly mattered, but several more could easily have gone in and this continues a run in which goals have been leaked with unusual regularity.

Three scares were survived with the game goalless and, after Claudio Pizarro's goal, Bayern hit the bar and had a header cleared off the line before Didier Drogba killed the match. The regularity with which Chelsea were exposed down the flanks and beaten in the air on crosses and set-plays in the second half was a worry.

Mourinho has been unfortunate to lose Paulo Ferreira and Wayne Bridge to injury, and cannot feel entirely comfortable with his situation at right back. Robert Huth was deployed there in this game, but did not convince, though Joe Cole worked impressively ahead of him to provide cover.

It is as well that Chelsea's leaking of goals has coincided with them finding the net with a useful regularity, but it would be interesting to see how the team would cope with Milan at the moment, in what could be a Champions League final.

Only a short while ago almost no doubt would have surrounded Chelsea's ability to withstand attacking barrages. Their backline, after all, was breached only twice in 14 games between December 18th and February 12th.

Yet of late their defence has been rather less secure, keeping one clean sheet in 10 attempts before this match, and it had been a sign of Felix Magath's confidence that the Bayern coach spoke beforehand of when, not if, his team took the lead.

In the end it took until the very last second, too late for it to matter, but Magath did detect signs of weakness for his team to exploit. The disappointment for him was that two chances inside the first five minutes were wasted.

Those both come from moves down Chelsea's right flank, where Mourinho had shown his concern about Glen Johnson's suitability for the occasion by dropping the former West Ham player and replacing him with Huth. That move left Chelsea with four central defenders across the back.

In those early moves Huth looked uncomfortably out of position, with Pizarro cutting inside him and Ze Roberto storming past to set up chances. Indeed, almost every time Bayern ran at Huth he looked vulnerable.

Yet Huth tried to operate in a narrow position, almost as a third centre-back, to deal with an expected barrage of crosses, rather than as a standard full-back. The plan as much as possible was to leave it to the wide midfielder, normally Joe Cole, or sometimes Claude Makelele, to close down players on that flank. Although Chelsea got to half-time without conceding, and were ahead courtesy of Frank Lampard's deflected goal, they suffered several worrying moments.

If John Terry deserves credit for blocking a shot by Michael Ballack and Petr Cech did well to save from Pizarro, Bayern will also wonder whether they might have been sharper. There were later occasions when Chelsea were opened up.

It seemed that the fizz was going from Bayern's play as their task at 5-2 down on aggregate became ever harder, but Chelsea's loss of their old impregnability was exposed by Bayern's three goals and numerous near misses. Mourinho has food for thought as he approaches the semi-final.