Speculation over Wednesday's blast ranged from an earthquake to an aircraft's sonic boom, but aviation authorities have ruled this out.
Activity at the MoD's Hebrides Range, a large live firing test site, has been suggested as the most likely cause.
One islander described how the big bang caused properties to shake.
Sheila MacCormick, of the Borrodale Hotel in South Uist, told BBC Scotland: "The actual building shook."
She said: "When we looked out there was people walking on the road - who were standing looking around to see what had happened.
"We didn't know what it was, couldn't see any signs of blasting - it was very, very loud to be a blast anyway.
"One of our bar staff put it on Facebook to see if it was heard anywhere else and we've had reports coming in from Benbecula and from Barra saying that they've also heard it."
BBC Scotland News Facebook users suggested the bang was a controlled explosion of out of date explosives and that some residents had received letters alerting them to activity at the rocket range.
A loud blast which was heard over Kent on Wednesday turned out to be the sound of RAF jets scrambled to intercept a Latvian cargo plane.
It has been suggested an MoD firing range may have been responsible for a huge bang heard as far apart as Benbecula and Barra.