Stroke affects millions of people all over the world, causing death and disability. The most frequent type of this disease is ischemic stroke, which can be caused by different factors. In approximately 25 percent of cases, no obvious cause can be found. Recent observations have shown that paroxysmal atrial fibrillation could be responsible for a significant number of cryptogenic stroke events. Short- or long-lasting ECG monitoring could help with the diagnosis of transient arrhythmias. Unfortunately, these techniques either are expensive or require good patient compliance. An alternative option is the identification of biological markers that are specific for atrial fibrillation and can be used to predict arrhythmia. In this review, we give a summary of the recent advances in the research of arrhythmia markers. Based on their structure and function, we differentiated four groups of biomarkers: markers of inflammation, markers of fibrosis, markers with hormonal activity, and other markers. In spite of intensive researches, the optimal biological marker is still not available, but there are some promising markers, like NT-proBNP/BNP.