Objective: Obsessions have been categorized as autogenous obsessions and reactive obsessions on the original of the cognitive theory and this study aimed to evaluate whether differences are found between obsessive compulsive disorder (OCD) subgroups in terms of biochemical markers. Methods: Thirty patients with obsessions defined as autogenous, 30 patients with obsessions defined as reactive group and 30 healthy volunteers were consisted the sample of the study. Sociodemographic Data Form, Yale-Brown Obsessive Compulsive Scale (Y-BOCS), Beck Depression Inventory (BDI), Beck Anxiety Inventory (BAI) were filled to the participants. The activity of paraoxanase, prolidase and Hs-CRP and brain-derived neurotrophic factor (BDNF) levels were detected. Results: There was no any statistically significant difference between autogenous and reactive obsession groups in terms of total mean score of Y-BOCS, BDI and BAI. Paraoxanase activity did not statistically significant difference between all groups. Prolidase activity showed significantly higher in reactive group than autogenous obsession and control groups. Serum Hs-CRP levels were not statistically different among participants of autogenous group, reactive group and control groups. Serum BDNF levels were significantly lower in autogenous obsession group rather than reactive obsession and control groups. Conclusion: This finding indicates that neurobiological processes have important role in the pathophysiology of autogenous obsessions.