When Miles O'Brien is trying to decode the ANA routine one of the sequences reads "GENE ROD", a reference to Star Trek creator Gene Roddenberry.
When Miles O'Brien is trying to decode the ANA routine one of the sequences reads "NCC1 701," a reference to Star Trek's famous ship, the USS Enterprise.
Colm Meaney considers "In the Hands of the Prophets" to be with "Captive Pursuit (1993)" as his other favorite episode from the first season.
Referenced Rules of Acquisition: #7 ("Keep your ears open")
This is the first episode of Deep Space Nine to deal with the Bajoran religion-political system, something which would become increasingly important as the series progressed.