Hi, Welcome to HCM. Chlamydia infection as such will not cause pain in vagina unless there is association of some other ulcerative condition inside your vagina. Chlamydia can cause a pelvic inflammatory disease which can cause a lower abdomen pain or pain during sexual contact. Passing thin stools, coming little by little and uncomfortable feeling during passing stools are likely to be symptoms of rectal stricture. This can occur very rarely in a STD called as Lymphogranuloma Venereum which is also caused by another type of Chlamydia. That type of stricture common in women with vaginal sex itself. But it is a sequence of a old untreated infection and not a fresh one. How long you are sexually active? This diasease is rare nowadays. So consult an expert in handling sexual disease, he/ she may be able to help you better. DR S.Murugan