It depends.

Your short term plan should be "qualified" as "major medical" and not just a discount or mini medical plan.

While your pre-existing may not be covered under the short term plan, you'll probably qualify for a continuation of coverage when you get onto a group or HIPAA plan.

Oh I see! what do you mean by HIPAA plan?

Title 1 of HIPAA, or the "Health Insurance Portability and Accountability Act" of 1996, provides that if you have exhausted all other options, had a continuation of coverage with no gaps, and will not qualify for any other Insurance, Health Insurance companies must offer you Health Insurance with no pre-existing exclusions. A HIPAA plan can be costly, but for some it’s the only option.

The key point here is you must exhaust all other options and have no gaps in coverage. In other words, you must first take COBRA for the full time it's available to you, usually 18 months.