In May of this year I started taking morning after pills and did so every month till August. I started having a brown dischare (light to dark in color) after my period it sometimes last up to 5 days after my period is supposed to end, I have had a pap smear and it showed LSIL, I have no infections as confirmed by my doctor, could the morning after pills be the cause of all this?

Holy crap! The morning after pill is an Emergency contraception method. It is not mean to be your ONLY method. Are you on the birth control pill or using condoms? In the long run it is cheaper and safer for your reproductive system.

Chances are the consistent use of the morning after pill is the cause of this. I can't be certain. When your got your pap did you tell the doctor how many times you had used the Morning After pill? You should also talk to him about other methods of birth control.