Obesity is one of the leading causes of morbidity and mortality worldwide. Obese women are at increased risk of developing Type 2 Diabetes, cardiovascular diseases, hyperlipidemia, rectal carcinoma and gynecological problems including sub fertility, menstrual dysfunction and polycystic ovarian disease. The aim of this study was to assess relationship of obesity with menstrual irregularity in young girls that can help to create awareness among young girls about obesity and how it can affect fertility. It was a case controlled cross sectional study comprising of 220 participants from different colleges and universities of Karachi and from outpatients department of private clinic and Civil Hospital Karachi. A questionnaire was designed to assess the relationship of obesity with irregular menstrual cycle. Questionnaires were filled by co-authors after taking verbal consent. Data was collected from March 2013 to December 2013 and entered and analyzed on SPSS 16.0. Out of 220 participants obese and overweight were 67(30.4%) and 49(22.2%) respectively. Significant association was found between body composition and menstrual cycle irregularity as menstrual irregularity was present in only 9.5% when the BMI was normal and 14.09% and 24% girls in the overweight and obese categories respectively. Waist to hip ratio was found increased in 61.36% of girls. Sixty four point forty four percent (64.44%) of the girls with increased waist to hip ratio reported menstrual irregularity which makes 39.55% of the total sample population. Dysmenorrhea was reported by 63.6% of participants and family history was positive in 77.3%. Hirsutism was reported in 36.7% and 49.2%, acne in 34.6% and 43.2%, weight gain tendency in 85.7% and 98.5%, types 2 diabetes in 0% and 4.4% and hypertension in 8.16% and 31.3% of overweight and obese participants respectively. This study shows considerable association between overall and central obesity with menstrual cycle irregularity. This study provides the grounds on which foundation of health promotion and awareness programs can be laid for targeted age group.