Background Early neurological deterioration (END) in acute ischemic stroke (AIS) can be associated with poor outcome. The aim of this study was to investigate the association between infarction subtypes, biomarkers and END, and to identify patients with risk of unfavorable functional outcome. Materials and Methods This prospective study enrolled 101 patients with AIS. Neurological status was evaluated according to NIHSS at acute onset, on days 2, 3, and 90. END was defined as ≥2-point increase of NIHSS within 72 hours. Functional outcome was assessed using NIHSS and the modified Rankin Scale (mRS) at day 90. Results END was observed in 20, 8%. Patients with large artery disease had higher risk of developing END compared with patients with cardioembolism or small vessel disease (p <0.01). Significant higher blood glucose level and leukocytes were observed in the END group. Patients with END had higher scores of mRS at day 90 (p <0.01). Levels of NSE, IL-6, hsCRP and NT-proBNP were higher in the patients with unfavorable compared with favorable functional outcome. Conclusion Large artery disease, high blood glucose and leukocytes levels are associated with END. Elevated levels of blood markers NSE, IL-6, HsCRP and NT-proBNP indicate poor functional outcome at 90 days after AIS. These patients must be identified and be offered treatment immediately in order to improve the functional outcome after AIS.