Introduction: Acute Flaccid Paralysis (AFP) can be caused by various causes including poliomyelitis and sometimes even Acute Encephalitis Syndrome (AES). The objective of this study was to study the clinico-epidemiological profile of different causes of AFP including AES and their associated co-morbidities. Materials and Methods: A prospective hospital-based study was carried out including all cases fulfilling AFP case definition. History, clinical examination, necessary investigations were performed and required treatment given. Regular follow-ups were done and final classification made alongwith AFP surveillance team. Results: Out of 43 children included in the study, 18 expired and 25 completed follow-up. Final classification showed 53.5% AES, 9.3% Guillain Barre Syndrome (GBS), 9.3% dyselectrolytemia, 9.3%, peripheral neuritis, 7% Non-Polio Entero Virus (NPEV) and 11.6% others. Fever, altered sensorium and convulsions were present in 79.1%, 65.1% and 58.1% respectively. Eightyfour percent had asymmetrical paralysis with quadriparesis in 72%. Cerebrospinal fluid was abnormal in 34.9%. Japanese encephalitis serology was positive in 4.7%. The mean GCS was 9.53±4.27 with a significant difference between survivors and non-survivors (p=0.02). Almost half (52.2%) required ICU care, of which 14 expired (p=0.005). Seventeen children needed mechanical ventilation, of which 13 died (p<0.001). Requirement of inotropes and complications like respiratory failure and autonomic failure were significantly related to death. Conclusion: AES, being one of the commonest causes of AFP, should be included in AFP surveillance. Poor GCS, requirement of inotropes, complications like respiratory failure and autonomic failure are related with poor prognosis.