A number of woodland plants are subject to the Botrytis fungus. I had a large patch of Cypripedium acaule that was decimated by it. The stems turned dark at the base and the whole plant then died. I would dig up the affected plants and take a close look at the entire structure including the rhizome. If you have a Master Gardeners group at the County Agent's in your county, you might take a sample in to them. I know that purists will shudder but when I determined the cause of my problem, I sprayed with a fungicide and was able to save an especially nice clump of nine plants. Desperate times call for desperate measures.

Ugh! I'll do as you suggest. We do have several locations nearby that are staffed by Master Gardeners. Thanks for the information.

Cathy

The brown color your eye perceives is actually 2 separate intermixed colors present in the leaves and stems, green from chlorophyll and red/purple from anthocyan. In some cases anthocyan will be predominant and the foliage/stems will be a purplish color.
I suspect what has happened to your Trilliums, is that the old rhizomes have suffered damage to their terminal buds, either physical, pests or disease. The stems you have are likely from offshoots of the old rhizome and are too immature to process all of the sugars produced by photosynthesis, the excess is producing anthocyan.

You will have to dig up the affected plants to determine if this is the case. If so, carefully remove all of the healthy offshoots, wash them carefully and replant in new soil, adding a small amount of fertilizer as a top dressing.
If the old rhizome has been damaged and some part of it is savable, cut off all of the damaged part and treat the remaining firm part as you do the offshoots.
Best of luck!
Rb

Rb, the clump in question has been moved within the past year or two. In addition, I've been doing some planting around it. It's very possible that the damage was caused by the physical trauma. Given this fact, does it make sense to leave the clump alone? Won't it recover better if left undisturbed?

Thanks
Cathy

If you think it is physical damage, then you are probably better off leaving them alone. They should recover, sometimes within a year or two, and begin producing green foliage. Strangely, the flowers do not seem to suffer any ill effects, even though the foliage exhibits a remarkable color change due to the anthocyan pigment.
Good luck!
Rb

Do you have a photo posted somewhere? My trillium leaves are turning brown too but that's normal since trilliums are a spring flower and are going dormant by this time of year. My seas of Blue Cohosh are also going yellow not for lack of watering but because they too are considered a "spring ephemeral" here in southern Ontario. Are you sure the brown is not just natural dormancy kicking in?

Knotty, I'm sure. I have quite a few clumps of trillium, and this browning is like nothing I've ever seen before. I haven't posted a picture to the web before, but I can give it a try.
sorry to be so slow to respond. I'm trying to set up a home business right now, so my days are extremely full. I just went out this morning to do some work in the garden, and found a weed that was 5' high. Since I usually keep the weeds under control, that was quite a surprise. But we have had wonderful weather for weeds, hot sun alternating with a few days of rain, so I guess it was to be expected.
Cathy