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Abstract Background There is lack of population level data on prevalence and distribution of common benign women’s health conditions such as endometriosis, uterine fibroids, polycystic ovary syndrome from the Eastern Mediterranean region despite their significant consequences on quality of life. In particular, there is complete absence of any health statistics from Northern Cyprus, which is an emerging region in Europe. The Cyprus Women’s Health Research (COHERE) Initiative is the first large-scale cross-sectional study in the region, aiming to determine the relative burden of benign women’s health conditions and related co-morbidities in women living in Northern Cyprus. Methods The COHERE Initiative is a cross-sectional study aiming to recruit 8000 women aged 18–55 years and residing for at least the past 5 years in Northern Cyprus. The study is composed of two main steps: (1) Baseline recruitment, including (i) completion of a detailed health questionnaire, which is an expanded version of the World Endometriosis Research Foundation (WERF) Endometriosis Phenome Harmonisation Project (EPHect) standardised questionnaire, including questions on demographics, menstrual history, hormone use, pregnancy, pain (pelvic pain, bladder and bowel pain, migraine), medical history, family history of illnesses, medication use, life-style factors in relation to a wide range of reproductive and endocrine conditions, resource use (ii) measurement of weight, height, waist/hip circumference and blood pressure, (iii) collection of saliva samples for genotyping. (2) Gynaecology clinic follow up, including a pelvic ultrasound scan (USS). There is also a follow-up food frequency questionnaire (FFQ) targeted to all women taking part in the baseline recruitment with an aim to collect more detailed data on dietary habits. Discussion The COHERE Initiative will generate prevalence rates for conditions, define the clinical profiles for women’s health conditions, and estimate the economic burden of these conditions in Northern Cyprus. The results will also provide insights into the current status of health-care among women living in a currently under-investigated region. The genetic findings will inform future gene mapping studies for investigation of the heritable component of conditions in this population/region. Moreover, the results will be compared with other centres collecting data using EPHect tools globally and will help determine population differences and similarities in disease patterns and clinical profiles. The COHERE Initiative will serve as a resource to conduct hypothesis-driven follow-up studies investigating effect of the ‘Mediterranean life-style’ as well as genetic factors on common benign women’s health conditions that maybe specific to Eastern Mediterranean populations.