General:
* Solitude
* Seclusion
* Loneliness
* Separation
* Alienation
* Quarantine
* Withdrawal
* Remoteness
* Exclusion
More specific:
* Confinement (physical restriction)
* Insulation (separation from external influences)
* Detachment (emotional distance)
* Marginalization (being excluded from mainstream society)
* Segregation (separation based on race, ethnicity, etc.)
The best synonym for "isolation" will depend on the specific situation and the nuance you want to convey.