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The band had kicked off the European leg of their eXPERIENCE + iNNOCENCE Tour on Friday at the Mercedes-Benz Arena in the German capital.
A video recorded by a fan and posted on Twitter showed Bono interrupting proceedings there on Saturday and telling fans in a hoarse voice: "I'm so sorry. Something has happened and I think we can't go on. It's not right for you. I'm sure this is not a big problem but I'm gonna have to do something."
He added: "If people want to go home, that's fine - we'll play another show for you another time ... Let's break, let's break for 10 minutes."
Clearly disappointed fans responded with a subdued applause as they walked off stage.
The band debuted the tour in North America in the summer after releasing their 14th studio album "Songs of Experience".
The band did not say if their September 4 show in the western city of Cologne would take place.
"Bono was in great form and great voice prior to the show and we were all looking forward to the second night in Berlin, but after a few songs, he suffered a complete loss of voice," U2 wrote on their official website.
"We don't know what has happened and we're taking medical advice."