Here is the thing....I am sure your doctor told you to refrain from any sexual activity (especially with a partner) for atleast 2 weeks. If not than he/she should have. What can happen is even if your taking the medicine you could give it to a partner thus your partner giving it back to you. If you have abstained from sex and have faithfully taken your medication as directed you will be fine. Generally if left untreated for more than 6 months it can be damaging. It varys on the person though.

You should, having or not sex in the meantime, have this checked and see if you are chlamydia free. It is much easier than wondering around if you had it or not, if you were going to spread it or suffer from infertility if it stays in the body.