A number of theories regarding the aetiology of Crohn's disease have been p
roposed. Diet, infections, other unidentified environmental factors and imm
une disregulation, all working under the influence of a genetic predisposit
ion, have been viewed with suspicion. Many now believe that Crohn's disease
is a syndrome caused by several aetiologies. The two leading theories are
the infectious and autoimmune theories. The leading infectious candidate is
Mycobacterium avium subspecies paratuberculosis (Mycobacterium paratubercu
losis), the causative agent of Johne's disease, an inflammatory bowel disea
se in a variety of mammals including cattle, sheep, deer, bison, monkeys an
d chimpanzees. The evidence to support M. paratuberculosis infection as a c
ause of Crohn's disease is mounting rapidly. Technical advances have allowe
d the identification and/or isolation of M. paratuberculosis from a signifi
cantly higher proportion of Crohn's disease tissues than from controls. The
se methodologies include: (i) improved culture techniques; (ii) development
of M. paratuberculosis-specific polymerase chain reaction assays; (iii) de
velopment of a novel in situ hybridization method; (iv) efficacy of macroli
de and anti-mycobacterial drug therapies; and (v) discovery of Crohn's dise
ase-specific seroreactivity against two specific M. paratuberculosis recomb
inant antigens. The causal role for M. paratuberculosis in Crohn's disease
and correlation of infection with specific stratification(s) of the disorde
r need to be investigated. The data implicating Crohn's as an autoimmune di
sorder may be viewed in a manner that supports the mycobacterial theory. Th
e mycobacterial theory and the autoimmune theory are complementary; the fir
st deals with the aetiology of the disorder, the second deals with its path
ogenesis. Combined therapies directed against a mycobacterial aetiology and
inflammation may be the optimal treatment of the disease.