Treatment must be applied before you see the problem because the purpose is to protect newly developing leaves.

So it's too late this year to treat.

Jean is correct on treatment, and that would be treatment for any of the rusts. Daconil or Mancozeb would protect new growth. Only one systemic is labelled for use by homeowners on fruit trees, which is mycobutonil, commonly sold as Immunox (just the fungicide, not the insecticide/fungicide), and works fairly well.

Treatments start to differ depending on exactly what kind of rust you have. Cedar-apple is fairly straightforward and easy to treat. Cedar-hawthorn rust is a bit more difficult to control. Cedar-quince is possibly the hardest to deal with since it can be an annual occurrence on rosaceous hosts.

I would talk to your Extension agent again about what kind of rust you have. Stem galls on Rosaceous hosts is pretty rare on cedar-apple rust. However, it's increasingly common on cedar-hawthorn and very common with cedar-quince rust. If your agent isn't familiar with the different kind of rusts, ask to have a sample sent off for proper diagnosis.

Cedar-Apple rust is one of those many plant pathogens that need two plants to survive. The host plant, a member of the cedar family somewhere within several miles of you, and your crabapple. My crabapples get this every year and it has not caused any problem and they fruit profusely and the Cedar Waxwings (and probably the Bohemian Waxwings) come in in late January and devour the now fairly well fermented apples. While it may look kind of not really great to have some leaves that are turning yelloow and dropping off the tree there is no real harm done and the people at your extension service office are quite corrrect in that you need do nothing, and even if you did it probably will not help much. The only people that may tell you that you need to spray something are those that have that something to sell, and the sprays seldom really do much good.

I am not a willy nilly chemical user, and at first I was thinking not to treat the rust if it was merely a cosmetic problem. I live in a very urban environment. But the presence of these spore cases on the back of the rust spots, plus the stem galls, plus the extent of the infestation has got me very worried. Thanks Stompede for mentioning that the stem galls may be a symptom of another type of rust. Perhaps it was misdiagnosed at Cooperative Extension. At the time I brought in the plant sample, the rust spots did not have the spores, and the stem galls were not there.

I suspect it was maybe NOT cedar apple rust since my cedars are not affected. Also, I have seen pictures of the cedar galls online and I don't have them--yet. I certainly don't want those galls deforming my cedar plants.

I try to use chemicals as little as possible, but I live in a row house in the middle of the city, I'm not surrounded by anything coming close to a balanced ecosystem. It is quite easy for disease to destroy my plants and run rampant. And yes I compost and tend to my soil and practice as good a hygiene as I can, which is why I'm wondering whether to tear out this tree. I would like to save it and my cedars if possible. But it may be too late this year? I guess once the spores are out the horse has left the barn, right?

Just because your junipers don't have galls doesn't mean you don't have rust on them. The galls are easiest seen in the spring with the horns. Otherwise, they are much smaller brown galls. Sometimes they will girdle the stem and cause dieback. Also, a juniper just needs to be within several miles of another host.

Something I forgot to mention is cultivar resistance to rust. I have not seen cedar-quince rust on 'Prairifire', 'Profusion', 'Cardinal', Golden Raindrops, 'Royal Raindrops', Molten Lava, or Red Jade, no matter how long I have them sitting next to infected hawthorns. I have seen many older cultivars get infected, though, and we are very limited as far as what we can grow in crabapples here, so the list of susceptible cultivars is probably greater.

Hosts of these rust can differ based on what kind it is. Cedar-apple rust can get on Malus. Cedar-hawthorn can get on apple/crab, hawthorn, serviceberry, pear, or quince. Cedar-quince will get on any of the above as well as Cydonia quince, not just flowering quince.

I would say the damage is typically aesthetic. However, damage can be severe enough that stems dieback. Also, 'Winter King' hawthorn has experienced nearly 100% fruit infection, making them worthless for winter attractiveness. Also, plants grown for fruit can take a hit. Apple and pear fruit is susceptible, but damage is proably more severe on serviceberry, where it is more troublesome than birds.

I looked last night but I cannot find any documentation on the variety of crabapple it was. I bought it from Forest Farm nursery and had it sitting in a pot for a year. I planted it out of sympathy not expecting it to take off the way it has. I do remember from making the decision to buy it that is was supposed to get between 8-12 ft., kinda shrubby and had little yellow fruits. I bought it for the fragrance, not the apples. I don't think it was Golden Raindrops. It is now easily 12 feet. It bloomed the first time this spring but very sparsely, and I don't see any fruit set probably due to the plant's struggles with the rust.

I've posted a picture so you can see that it is really a specimen plant in the middle of an urban island. You can see the jupipers next to it on the left. The apple is the little thing staked to the pencil thin stake. The trunk is the size of my wrist now, two years later, and the tree towers over everything in that bed. Also, everything in the bed is now 2-3 times larger. They all looked so cute as babies, lol! The apple is intended for sort of an espalier application. I don't want to shade out my neighbors garden on the other side. The rose on the right I had to tear out as it grew into a behemouth bramble sending out suckers to my yard and the neighors, meanwhile not blooming in a very showy way.