The aim of this study was to assess the impact of consanguinity on risk for mental disorders especially in primary health care-PHC settings. It was decided to ascertain prevalence of common mental disorders and consanguinity. We set out to study the burden of commonest psychiatric disorders among consanguineous marriages at PHC using the WHO Composite International Diagnostic Interview (WHO-CIDI) and examine their symptom patterns and co-morbidity in Qatar. A prospective cross sectional study was carried out over a year between November 2011 to October 2012. A total of 2.000 Qatari subjects aged 18 to 65 years were approached; 1.475 (73.3%) gave consent and participated in this study. Prevalence of psychiatric disorders using the WHO Composite International Diagnostic Interview (CIDI, version 3.0) showed that six most common disorders were major depression disorders (18.3%), any impulse control condition (18.3%), any anxiety disorders (17.2%), any mood disorders (16.9%), followed by separation anxiety disorders (15.2%), personality disorder (14.1%). The mean age ± SD of the 1.475 subjects interviewed was 39.3 ± 9.8 years. The rate of consanguinity in the present generation was 31.5% [95% CI = 29.1–33.7]. There were statistically significant differences between consanguineous and non-consanguineous with regards to age, educational status, occupation status, household income as well as BMI, cigarette smoking and sheesha smoking. One-fifth of all adults who attended the PHC center 20% had at least one psychiatric diagnosis. The prevalence of the generalized anxiety disorders; social phobia, specific phobia, major depression, and personality disorders were significantly higher in consanguineous marriages than in non-consanguineous.