Small extracellular vesicles (sEVs) properties and sEVs composition are far from being well-studied for now, especially in the context of mental disorders. To elucidate the role of sEVs in disease we performed a quantitative analysis of the blood sEV in patients with focal epilepsy and patients with focal epilepsy with depression, psychogenic non-epileptic seizures with depression, pure depression, and bipolar affective disorder with the current depressive episode (cDE). Small EVs were isolated from the serum by gel filtration or PEG precipitation, and both methods showed very similar results. Subsequently, we precipitated neuronal sEVs and quantified it with several methods. Activity of lysosomal enzymes was determined in the sEVs fraction. The concentration of the blood sEVs in patients with depression, focal epilepsy, or depression with focal epilepsy was higher than in healthy controls. No difference was found between patients and controls in terms of neuronal sEVs concentration. Another finding of our work is that sEVs in the serum of patients contains various lysosomal enzymes. We suppose that the concentration of the blood sEVs in patients with depression or epilepsy is higher due to the sEVs secretion by the immune cells. Finding sEVs in the blood of patients with depression and focal epilepsy grants validity for future attempts to use sEVs as diagnostic tools for these disorders.