Introduction Obstructive sleep apnea syndrome (OSAS) is a common disorder that has a major impact on public health. The connection between OSAS and obesity is very complex and likely represents an interaction between biological and lifestyle factors. Oxidative stress, inflammation and metabolic dysregulation are both actors involved in the pathogenesis of OSAS and obesity. Also, the current evidence suggests that gut microbiota plays a significant role in the emergence and progression of some metabolic disorders. When the relationship between OSAS and obesity is evaluated extensively, it is understood that they show mutual causality with each other, and that metabolic challenges such as impaired microbiota affect this bidirectional organ interaction, and by ensuing organ injury. Objectives The aim of this study is to investigate the association between OSAS and obesity, and the effect of "organ crosstalk" on the pathogenesis of the relationship and to contribute to the diagnosis and treatment options in the light of current data. Data Source We performed an electronic database search including PubMed, EMBASE and Web of Science. We used the following search terms: OSAS, obesity, inflammation, metabolic dysregulation and gut microbiota. Conclusion Obesity and OSAS adversely affect many organs and systems. Besides the factors affecting the diagnosis of the OSAS-obesity relationship, mutual organ interactions among the respiratory system, adipose tissue and intestines should not be ignored for prevention and treatment of OSAS and obesity. Comprehensive clinical trials addressing the efficacy and efficiency of current or potential treatments on therapeutic applications in the OSAS-obesity relationship are needed.