I'm a beginner gardener, and growing tomato plants for the first time. I need help diagnosing a problem on my stems!

I regrew my three plants from seeds of a small heirloom tomato that I came across last year. All three plants are still indoors and small-ish. I labeled them in the below pictures as A/B/C. Sadly, the stems are all showing signs of deformity, though leaves don't have major issues (maybe a light yellow spot or two, which I plucked off). Plant C's stem was looking healthy until recently, and now it's starting to get that scabby look and lose its hairy quality in the affected area. Is this early blight? Bacteria?

Plant C was healthy looking until recently. Should I separate plant C from the others, or is it too late?

I've learned a lot already through this process and in hindsight probably should've heat treated those seeds. Would love help in diagnosing in the meantime. Thanks!

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  • Were these plants always indoor? Jun 10, 2020 at 7:33
  • Yes, sadly. Trying NYC indoor gardening, no outdoor garden option available!
    – hamcake
    Jun 17, 2020 at 21:41

2 Answers 2


It looks like they may have gotten sprayed with something toxic to them, like a cleaner or disinfectant....it looks like it killed part of the stem.

That's a possible cause, the effect is some die-off of stem tissues, regardless of how.

Tomatoes will root all along the stems where they are in contact with soil. I've even rooted cuttings as an experiment.

To be safe, you could plant them deeper, with soil levels above the damage, they almost certainly root above the damage & quite probably be stronger.

if you unstake them and let them flop over naturally, the same thing will happen also.

Hope that helps

  • Thank you!! Will try that!
    – hamcake
    Jun 17, 2020 at 21:40

I just googled for this same issue! I’ve grown tomatoes for years and have always started indoors as well. I’m started this season from previously very successful seeds, from which I’ve never had issues outside of normal tomato pests. Today I look and see the same issue as yours with every one of my seedlings. I for sure have not sprayed anything like a cleaner in that room, so I don’t think that was it. What DID happen was my 6 year old son ran his hands through the seedlings one day pretty aggressively. That was about a week ago, and although they seemed fine, I am guessing that was the cause. Do you have kids or any pets that may have damaged the stems cell walls? I like the idea of burying them below the damage, I was ready to get rid of them knowing that weak stems would just invite pests and disease.

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