What special unique place do most tourists overlook in Venice?

How long and when will you be in Venice?

3 nights next month. Thanks. I should have included that.

I don't know if many people visit Torcello while taking in Murano and Burano...

There are two special places we always include on our walks around Venice, however long or short our stay. One is the beautiful Chiesa Santa Maria dei Miracoli:

https://en.m.wikipedia.org/wiki/Santa_Maria_dei_Miracoli,_Venice

And the other is Punta della Dogana on the tip of Dorsoduro. Rick mentions the museum there but not the viewpoint itself.

I have never actually been inside the church; I just love seeing it from the outside. But it is one of the Chorus churches, so well worth a visit inside.

My favorite campo is San Giacomo dell'Orio in San Polo. On weekends you may find a neighborhood festival there as we did.

Thank you Lola and Nicole! I appreciate your suggestions and links! We are very much looking forward to our first visit to Venice.

Just got back from our 8th trip to Venezia and we did find some new-to-us places. The Scuola Grande di San Marco in the public hospital at Piazza SS Giovanni & Paolo has a medical museum that is quite interesting, and the building itself is a work of art. Not many make it to Torcello and we find that charming on a sunny day.

Restaurant discoveries this trip: Osteria si Santa Marina, Impronta Cafe, and Osteria Ai Promessi Sposi. Make reservations by all means (some are possible online). We also return each trip to NoNo Risorto and Birreria Forst (lunch). Across the street from Birreria Forst is another sandwich shop we like, but the name eludes me right now. Trattoria Bar Pontini near the Ghetto is also worth a stop.

Three nights is two days, you don't even have time for the typical tourist stops. Still, I would spend one morning or afternoon just wander aimlessly as far as you can go -- Venice gets more picturesque and interesting the farther you get from the center and you can't get lost because eventually you run out of islands. Just ask a local 'San Marco? per favore' and they will point you back towards the center.

Lots of typical tourists waste too much time in San Marco - getting as far away from San Marco as possible is definitely my recommendation.

Torcello and the Ghetto.

Thanks for all your suggestions. We actually have the better part of 3 days because we get off a cruise ship around 8am, which gives us the rest of that day and the next two full days before we take the train out of town 3 days after our arrival.

Museo di Storia Naturale di Venezia! Venice's natural history museum has their lone dinosaur wonderfully displayed in a room encircled with video of the actual dig in Africa. There are also banks of glass-front cabinets with artistic collections of specimens, a room-size Wunderkammer (cabinet of curiosities), and a horrifying room of big game trophies and photographs. It's not the easiest place to find, but the San Stae vaporetto stop is closest. Once you start down the narrow alleys, you'll probably have to ask for directions at least once. The nearby piazza is a quiet oasis where Venetian children play, and there's a fine bakery for take-out. (This is probably not a top tier site on such a quick visit, but go see it someday.)

Not sure it's overlooked, but I liked the Peggy Guggenheim Collection in the Dorsoduro area. It's a modern art museum.

A very moving but often bypassed place to visit is The Ghetto.

I really enjoyed Santa Maria Gloriosa dei Frari church...I can't really pinpoint why I liked it so much - maybe the art...maybe the funeral monuments (Canova's heart is buried here - which I found very fascinating - don't know why that one thing has stuck with me all these years!). A lot of times I go into churches I just give the paintings cursory glance, but something about this church really made me stop and look...

The Sacristy of the church of San Polo. A really special Stations of the Cross. Painted by Tiepolo.

I love everyone's suggestions - it's amazing how much there is in Venice that holds special memories. I know you don't have much time and maybe Torcello is a bit far (unless you are already going to Murano and Burano) but the two churches there absolutely took by breath away! My other favorite is to turn left (unless I have to turn right) down an alley or path I haven't been down before. You might hit a dead end but you can truly say you've seen something/someplace very different than home. Get far away from Rialto and San Marco as soon as you can. In my opinion, museums are for 'looking at art' while Venice is for 'walking in the art.'

Another vote for the Frari church which is lightly visited. Our visit to San Marco was pretty awful, barking rude staff and fairly unattractive interior.

I couldn't even tell you what we saw while in Venice. But, when we saw a crowd we turned the other way and headed down a narrow street without people. We walked miles and miles just exploring nooks and crannies without people. We found a fabulous smelling restaurant that had 4 tables. We didn't have a reservation so we made one for the next night. But, we could never find it again so we missed out!

We did do St. Marks square but late at night, into St. Marks early, and toured the palace and took a vaporetto to Burano and Murano. We enjoyed the islands, but really most of all, just wander off far from tourists.

The Po Delta and all the islands around Venice. There are many but some are only reachable by private boat.

There are lots of such places, but this one comes to mind in an article for the NYT written by a friend of mine:
Venice's Jewish Ghetto

Thank you to everyone who made suggestions for me on "special unique places" most tourists overlook in Venice.

We disembarked the NCL Jade cruise ship there May 2nd and water taxied to our hotel by Ponte Testolini for a 3-night stay. We signed up for 4 Viator tours, including 3 of them in one day.

Tour to Murano-Burano-Torcello: We had a beautiful sunny day for this and enjoyed it very much. Thanks for the recommendations. Murano wasn't much -- just a drop-off to watch one artisan demonstrate how to make a couple beautiful glass pieces, then you get ushered into the shop to spend money. We enjoyed the demonstration -- and the shopping! -- but wish it was more like the Waterford crystal tour we did in Ireland where you walk thru the plant and watch many artisans at work. Burano was a beautiful waterside village with good shops and restaurants. Torcello has interesting religious structures and several bars and restaurants between the dock and the church area. The church and mosaic wall are definitely worth the visit. A very relaxing and enjoyable boat tour to these 3 islands in the Venice lagoon.

Walking tour of the Doge's Palace - Very informative with lots of interesting history very well-presented.

Walking tour of Venice -- A very brief (5-10 minutes) walk thru of St. Mark's Basilica ( a little too short) but then a fascinating walk thru many of the out-of-the-way sidestreets of Venice. Wonderful tour guide (actually, all the Viator guides are excellent). Liked seeing the ospedale/hospital with the water ambulances and water hearse parked in the canal alongside.

Speedboat tour of the canals - A one-hour water taxi ride for just 8 tourists with one guide. We zoomed all over the place, this was a lot of fun and interesting.

Other things we did that were recommended here for us: Frari Church - very interesting historically and artistically, definitely well-worth the visit. Jewish Quarter -- we kind of got here by making a wrong turn walking somewhere else and found this area to be away from the tourist hordes and very interesting.

We had a wonderful dinner at the Antico Caffe next to the La Fenice opera house. A Mozart opera was playing and we really enjoyed having dinner with a view of the exterior facade of the theater, watching as patrons came outside at intermission, and then again at the end of the performance (yes, we were still in the restaurant). Delicious dinner plus we loved watching the theater and the theatergoers right next door.

And, for a spectacular view, we recommend having a drink at the Hotel Danieli rooftop bar right next to the Doge's Palace. Open air view over Venice lagoon looking directly at Saint Giorgio Maggiore cathedral and other beautiful Venice sites. Expensive drinks, and cover your snacks so the pigeons don't dive-bomb your table, but a wonderful view.

I completely understand those who say to just "walk the city" and explore away from the tourist highlights. Those highlights are worth seeing, but experiencing Venice "behind the scenes" is a truly wonderful experience. We thoroughly loved our visit and very much appreciate all the suggestions. Thank you!!

We stayed in an apartment in the Jewish ghetto. We enjoyed walking the neighborhood. Well worth a visit.

I stopped at San Michele, Venice's cemetery island, on the way to Murano. Enjoyed walking around looking at the cemetery. They take very good care of the graves and many were decorated with fresh flowers. I also was able to see a boat pull up, unload a coffin and mourners for a funeral.

It was worth a stop on the island to see the lovely grounds.

The Squero di San Trovaso boatyard, where gondolas are built and repaired, is viewable from across a small canal. You can take an audio tour of La Fenice opera house. Lola mentioned the Chorus Pass - you can get one at any of the participating churches, and finding them all will take you all over the city.

What first got me interested in the La Fenice (The Phoenix) opera house was at the start of our trip (Barcelona airport, I believe) picking up a mystery book called "Murder at La Fenice" by Donna Leon, the first in a series of Commisario Brunetti mystery novels set in Venice. The book opens with the opera conductor found poisoned in his dressing room at the second intermission of "La Traviata", and so as an opera/mystery/travel afficionado, I had to see La Fenice. What a great find with the excellent restaurant next door. We didn't know about the audio tour of the theater while we were there so we didn't do that. I peaked inside the lobby during one of the intermissions/intervals and got a good look at the lobby before being asked to leave (only ticket holders were allowed in).

Here's another vote for Frari Church. RS has a free audio download tour of Frari which we used. You can check it out before your trip to see if Frari interests you. Also, the San Rocco complex is a lovely, uncrowded sight. The RS guide gives details. You can also Google it. It's a church and art museum combined in two buildings on a small piazza.

I know the OP already took their trip, but in case anyone's looking at this for ideas, I second San Michele (the cemetery island).

It was interesting to read in the first Donna Leon "Commisario Brunetti" mystery that autopsies are or were performed at an official location on San Michele. Other facts: Igor Stravinsky and Ezra Pound, among other famous people, were interred there. Also, apparently bodies are only buried there for around 10 years then moved to an ossuary or other site to make room for "newbies" coming in. We saw the island from the water on our recent visit but did not go there.

I have a suggestion, perhaps not a place, but activity.

Get up early and watch the city come to life. By early I mean 5:30 or so. Find a side canal with businesses or hotels that stems off the Grand Canal. It is quite interesting to see how commerce develops on the canals. How the businesses are supported by deliveries. How products move across the bridges and under the bridges. When you thin about what we, on land, take for granted it is pretty incredible how Venezia has developed is efficient systems.

Yes to all the above but don't forget a late night ride up and down the Grand Canal. What a relaxing and romantic end to the day!