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After several false starts, I've finally started being able to get some regular exercise in post-baby, who was born 8 months ago. I'm 34, still breastfeeding and had an EMCS if any of those thing are relevant.
I'm basically cross-training and circuit/interval training using DVDs and doing a lot of walking with the pram. I was careful and did a gradual build up back to the high-impact stuff, and I'm still using very light weights (2kg) but my knees just ache! I was a pretty hard-core exerciser pre-baby, including all through pregnancy, and I've not had this before. It's a dull ache around my patellae - my knees feel like they're going to buckle when I'm going up and down stairs. I'm religious about warm-ups, cool-downs and stretching. Because of DS, I don't have other exercise options apart from DVDs and walking, if I want to maintain it once I go back to work in two weeks (e.g. can't swap to a no-impact alternative like swimming).
I swear my knees hurt more when I have my periods. I do lots of sports but I can't seem to find a link between that and when my knees play up. Sorry, that is not much help! I just think it is interesting.
You are probably best seeing your GP or going to a sports injury clinic.
I think it's still a bit too much of a first world problem at this stage for the GP (oh, doc, I can't do squat jacks the way I used to!). I was wondering if it had something to do with joints still being a bit hypermobile post-pg or summat...
I work cheek by jowl with physios so I'll pick their brains if no-one here has any ideas.
I had a similar problem after DD2, when I went to the physio he said that all that lovely hormonal stuff you get in late pregnancy which makes your joints more flexible is still in your body for up to a year after birth. This means that your knees and bits can get a bit sore and injured more easily (I think). Anyway, he gave me a set of exercises that were fantastic, and some painful massages and charged me £40 an hour (!) but it did work and any time I get sore now I repeat the exercises. They were called open leg book exercises... I think.... but probably better to ask an expert!