Jennifer Garner's opening narration which was used throughout Season 1 was literally phoned in. She was working on location and had to read it down the phoneline to J.J. Abrams who was recording it on the other end.
In season 4, episode 3, at Weiss' birthday party, while Sydney and Jack are talking outside, a song called "You All Everybody" can be heard playing inside the house. This song is the made-up hit single of Drive Shaft, the fictional band of Dominic Monaghan's character Charlie on Lost (2004), another series by Alias creator/executive producer J.J. Abrams.
The number 47 is used repeatedly throughout the series. Examples: Marshall expresses a desire to improve a camera design so that it has 47 exposures; the key code Will needs to get into a computer room in order to retrieve data on SD-6 is 4747; the crate at the Vatican which contains the painting with Rambaldi's cipher-key has a 5-digit catalog number ending in 47; page 47 is always significant in a Rambaldi manuscript; and of course, there are 47 parts to Rambaldi's magnum opus. In episodes of season 3, Sydney tries to retrieve memories of when she is abducted, as she is dreaming... Masked men take her in to a room with the number 47 largely printed on its doors. And also in the dream she sees fireworks when she looks through the window as a reference to 4th of July (4/7). Interestingly, the Star Trek TV shows also feature the number 47 many times (it's usually seen in their monitors). Also server 47 is the number of the server that Sydney needed to get information from to take down sd-6. Ramboldi
Creator J.J. Abrams says the idea for the show came from a half-joking story plot for his series Felicity (1998). Abrams considered an episode where Felicity spends her summer as a government agent, then returns to school the next fall like nothing ever happened.
Alias has some references to "Alice in Wonderland". For instance, when Sydney returns from her two year absence, she moves into a new house since the old one burned down. Weiss asks her what is the one thing she wishes she hadn't lost (other than Vaughn), she says the first edition of "Alice in Wonderland" that her mother gave when she was little. So Weiss gives her a third edition (because he says the first edition cost way too much) to make her feel better. This is interesting because Sydney is an Alice herself going deeper and deeper into the rabbit hole. In season 1, Sydney dressed up like Alice for Halloween; in season 4, Vaughn is directed to "through the looking glass" when he is searching for something in the library, and in the season 1, Vaughn has a girlfriend named Alice. On Masquerade, Sydney's code name is White Rabbit.
For her birthday, star Jennifer Garner was given a pink bicycle by series creator J.J. Abrams. Being the first one on set, she would often greet the production crew by ringing the bells on the bike's handlebars.
During the opening credits, the Rambaldi symbol is flashed over the "Alias" logo for exactly one frame. During at least the first season, this happens while Victor Garber's name is on screen. Also, the images moving behind the logo are home movies of creator J.J. Abrams' children during a 4th of July celebration.
In-joke: After Will and intern Jenny become lovers in an early episode, Francie chides him for dating a cheerleader. He replies that she isn't a cheerleader ... anymore. Sarah Shahi who plays Jenny was, in fact, a popular Dallas Cowboys cheerleader until not long before the series began.
Rachel Nichols' character was created for two specific reasons: 1) Knowing it was the last season, writers wanted to pay tribute to the series by repeating Sydney's first plot (an agent discovers that is working for the enemy she believed was fighting) and 2) The show needed a new action character because of Jennifer Garner's pregnancy.
The Rambaldi prophecy is: "This woman here depicted will possess unseen marks. Signs that she will be the one to bring forth my works. Bind them with fury, a burning anger unless prevented at vulgar cost this woman will render the greatest power unto utter desolation."
In season 1 when Will Tippin (Bradley Cooper) is down in the docks snooping around, he passes a freighter ship. The name of the ship is "Alba Varden", that is also the name of the ship from "Lethal Weapon 2" where the final battle takes place.
In Joke: In the pilot episode, when Sydney is caught sneaking around at the party, she lies to the guard, by saying that she will get in trouble with her boss "Ron", if he finds out she'd been drinking. Her boss at SD-6, Arvin Sloane, is played by Ron Rifkin.
Sark asks Sloane for a glass of "Chateau Pétrus, 82" in return for his cooperation in finding Khasinau. Chateau Pétrus, is in fact, one of the world's rarest and most expensive wines. The Chateau Pétrus Pomerol, a Merlot, is described as one of the greatest wines of the vintage and will set you back between roughly $7,000-$10,000 per bottle
After episode #2.13 (Phase One) the show's prominent use of cliffhangers at every episode's end was abandoned for a more traditional (one episode, one story) way of storytelling. This was apparently done due to demands from ABC TV execs who were under the impression that new viewers wouldn't "get" the show and feared the drop of ratings.
The two-part episode, "The Box" where rogue agents take over SD-6, has a plot similar to Die Hard (1988). The van that the rogue agents pull up in has the name McTiernan written on the side. John McTiernan was the director of Die Hard.
Marshall's gadget, the small disc that can knock someone out just by touching skin - he describes it "like freebasing Thorazine". Chlorpromazine (Thorazine) is an anti-psychotic drug, used in the treatment of disorganized and psychotic thinking, and the treatment of false perceptions (e.g. hallucinations or delusions.) Drugs of this type are commonly used in mental institutions for patients who do not have a comfortable grasp on reality.
In season three, when Sydney sees her name on the "Agents Killed in Action" plaque, the name directly below hers is "Scott Chambliss". Scott Chambliss is actually an award-winning production designer on the show.
Sydney says to CIA Agent Michael Vaughn, "The L.A Kings are in town next week." She also says that they are playing the New York Islanders, and she suggests that they go. This episode was aired January 20th 2002; the Kings actually played the Islanders one night before this episode aired.
Director Ken Olin and writers Jesse Alexander and Jeff Pinkner are the only crew members that directed or wrote episodes in every season. Olin directed 23, Alexander wrote 11 and Pinker 12, including the series finale.
The trivia items below may give away important plot points.
Lena Olin was never fired from the show, nor was her character written out as a result of a contract dispute. Lena Olin did not want to rejoin the cast because she lives in Manhattan with her family and did not want to commute back and forth to Los Angeles for filming. To "cope" with Lena's departure, her character was killed off at the hands of Jack. Afterwards, Lena was available, and Irina was revealed to be alive.
Five different actresses have played Laura Bristow/Irina Derevko. Arabella Holzbog played Laura Bristow in a picture Sydney kept. Kate Anthony was the voice of Irina Derevko in the video clip shown in episode 1.19, "Snowman". Natasha Pavlovich is the woman we actually see as Irina Derevko in that video clip. April Webster played Irina when she walks up to Sydney at the end of episode 1.21, "Almost Thirty Years". Finally, Lena Olin played Irina Derevko for the second season and beyond. Additionally, in Season 4, episode 18, Sydney Bristow (Garner) briefly portrays her mother (Laura Bristow) so they can learn information from her father.
In the season 1, episode 15, Will Tippin has been taken to a warehouse by Jack Bristrow. After they got there, Jack showed a picture of Will's parents. Actually it's Bradley Cooper's parents in that picture.