Even though married, I file a separate return from my spouse. Does this affect my ability to claim the low-income housing credit?

No, filing status has no impact on eligibility for the credit. Owners of residential low-income rental buildings can claim a low-income housing credit over a 10-year period. You can learn more about the low-income housing credit from the U.S. Department of Housing and Urban Development at http://portal.hud.gov/hudportal/HUD?src=/program_offices/comm_planning/affordablehousing/training/web/lihtc/basics.