Can having cysts in your ovaries cause irregular periods? Ive been having a period (light) every 2 weeks for 5 months now. This happened last yr and I got checked out found I had 3 cysts in one ovary and 1 in the other but said nothing to worry about. I thought it was due to methotrexate or prednisolone so reduced the dose and things went back to normal for a good few months but now it's gone like this. The problem been that every time I have a period it really aggravates the sle so twice a month is so irritating and painful I'm not sure what to do I'm only getting 1 wk where I feel semi-normal!! Any advice would be great fully appreciated so I'm armed for the doctor.