You can still get service connection for a pre-existing disability if you can show that it was permanently aggravated during military service. The boilerplate legalese language is:
A preexisting injury or disease will be considered to have been aggravated by active service where there is an increase in disability during such service, unless there is a specific finding that the increase in disability is due to the natural progress of the disease. 38 U.S.C.A. § 1153; 38 C.F.R. § 3.306(a). Aggravation may not be conceded where the disability underwent no increase in severity during service on the basis of all the evidence of record pertaining to the manifestations of the disability prior to, during, and subsequent to service. 38 U.S.C.A. § 1153; 38 C.F.R. §§ 3.304, 3.306(b). A preexisting disease or injury will be presumed to have been aggravated by service only if the evidence shows that the underlying disability underwent an increase in severity; the occurrence of symptoms, in the absence of an increase in the underlying severity, does not constitute aggravation of the disability. Davis v. Principi, 276 F.3d 1341, 1345 (Fed. Cir. 2002); 38 C.F.R. § 3.306(a).
Aggravation for purposes of entitlement to VA compensation benefits requires more than that a preexisting disorder become intermittently symptomatic during service; rather, there must be permanent advancement of the underlying pathology. Aggravation is characterized by an increase in the severity of a disability during service, and a finding of aggravation is not appropriate in cases where the evidence specifically shows that the increase is due to the natural progress of the disease. Furthermore, temporary or intermittent flare-ups of a preexisting disease during service are not sufficient to be considered aggravation of the disease unless the underlying condition, as contrasted to symptoms, is worsened. See Jensen v. Brown, 4 Vet. App. 304, 306-07 (1993); Hunt v. Derwinski, 1 Vet. App. 292 (1991); Verdon v. Brown, 8 Vet. App. 529, 536-7 (1996).
What this basically means is that you need to get a doctor to give you a medical opinion that your Crohn's got permanently worse during military service. If you can prove that, you'll get service connection just as if it had started in service. For you, I recommend the following steps:
1) Get in touch with a vet rep agency such as DAV, VFW, VVA, etc. They'll give you more info on what to do and what evidence you need.
2) Get a private doctor to look you over and give a written opinion about whether your Crohn's was permanently aggravated by military service. Make sure he conducts a full exam before giving the opinion AND make sure he reviews all of your old medical records, especially your service medical records. Make sure the doctor gives a detailed explanation of WHY he thinks your Crohn's was permanently aggravated, citing your own medical history and current medical knowledge if at all possible. Send this report to VA with your claim.
3) If you do the above, VA will likely schedule you for an exam of their own to get a VA doctor opinion on the issue. If the doctor agrees with the private doctor, your claim will likely be granted. If he disagrees, your claim will likely be denied. If it is denied, (promptly) appeal the claim properly up to the Board of Veterans' Appeals. Your rep can help you with this.