Consanguineous marriage (CM) is a prevalent kind of relationship in Muslim and Arab countries, and this type of relationship is linked to several health risks. This study was conducted to determine the prevalence of (CM), its associated hereditary diseases, and health-related issues among Saudi citizens in Albaha. This cross-sectional study was conducted between March 2021 to April 2021. Saudi citizens in Albaha who were aged ≥ 18 years and willing to participate were eligible for the study. A total of 1010 participants were included in this study. In total, 757 participants were married, widowed, or divorced. CM partnerships comprised 40% (N = 302) of the marriages among participants, of which first- and second-cousin marriages comprised 72% and 28%, respectively. The prevalence of CM among the participants’ parents was lower than that among the participants (31% versus 40%, respectively). Children of participants in a CM were more likely to have cardiovascular diseases (p < 0.001), blood diseases (anaemia, thalassemia) (p < 0.001), cancer (p = 0.046), hearing loss and speech disorder (p = 0.003), and ophthalmic diseases (p = 0.037). Albaha showed a high percentage of consanguinity. An educational program must be established to enhance the population’s knowledge of the consequences of CM. The current national premarital screening program should be extended to involve more screening tests for common hereditary diseases that result from CM.