Paliperidone, is a known orally active antipsychotic agent. Five related substances (Impurities) were observed during laboratory process development and pilot scale preparation of Paliperidone. They are Didehydro paliperidone, 9-Alkyl analogue, Dehydro-9-alkyl analogue, Desfluoro paliperidone and Hydroxy keto paliperidone. The present work describes the detection, origin, synthesis, characterization and control of these related substances, thereby providing a commercial method to synthesize substantially pure paliperidone.