http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2861306/

Causes of persistent problems

1. Dewar DH, Donnelly SC, McLaughlin SD, et al. Celiac disease: management of persistent symptoms in patients on a gluten-free diet. World J Gastroenterol 2012;18:1348–56

Dr. Thompson made some good points about Refactory Celiac Disease.  Table 2 is from his slide presentation.

The top chart is what I found on the government website, including the text below.

Celiac disease (CD) is an immune-mediated disorder affecting genetically
predisposed subjects, caused by the ingestion of gluten present in cereals such
as wheat, barley and rye.1 CD affects around 1% of the general population in
developed and developing countries, with increasing prevalence over time
reported in the United States and Europe.2–4 Lifelong gluten-free diet (GFD) is
the only effective treatment to alleviate the symptoms, normalize antibodies and
the intestinal mucosa in patients with CD.5

Clinical response is observed in most patients with CD after only few weeks on a
GFD .6 However, complete clinical response and mucosal recovery does not occur in
all patients with treated CD. 7 Indeed, a subgroup of patients with CD may have
persistent or recurrent symptoms (e.g., diarrhea, abdominal pain, and weight
loss), inflammation of the intestine, and villous atrophy despite strict
adherence to a GFD.8, 9 Symptoms are often severe and require additional
therapeutic intervention besides GFD.5, 8 Refractory celiac disease (RCD) is
defined by persistent or recurrent malabsorptive symptoms and villous atrophy
despite strict adherence to a gluten-free diet (GFD) for at least 6–12 months in
the absence of other causes of non-responsive treated celiac disease (CD) and
overt malignancy.10–12 The aims of this article are (1) to review recent
advances in the diagnosis and management of patients with RCD and (2) to
describe current and novel methods for classification of patients with RCD into
categories that are useful to predict outcome and direct treatment. See the chart above*

Epidemiology (How often does it occur?)

The real prevalence of RCD is unknown but is probably rare. Evidence of the
rarity of RCD is the low number of cases reported in the literature, most often
from major CD referral centers.13–18 However, RCD may be the cause underlying
persistent or recurrent symptoms in treated CD in just 10 to 18% of the patients
evaluated in referral centers.10, 11

Estimates of the occurrence of RCD in non-referral, population-based cohorts are
very scarce. RCD was diagnosed in only 5 (0.7%) of 713 patients with CD from the
Derby cohort (United Kingdom) from 1978 to 2005.19 From 204 biopsy-confirmed CD
residents of Olmsted County (Minnesota, United States) identified from 1950 to
2006, only 3 (1.47%, 95% CI: 0.3%–4.2%) had a subsequent diagnosis of RCD type 1
(n=2) or type 2 (n=1). The incidence per 100,000 person-years was 0.06 (95% CI:
0.0–0.12) adjusted for age and gender to the 2000 US white population. (A.R-T,
unpublished data 2009) Thus, RCD appears to be an uncommon condition but with a
poor outcome.1

RCD affects two to three times as many women than men,13, 15, 17 consistent with
the predominance of diagnosed CD in adult women.1 The predominance of disease in
women diminishes somewhat in those patients with both RCD and EATL.13, 17 RCD
diagnosis is exceptional before the age of 30 years and most cases are diagnosed
around the age of 50 years or thereafter.15, 17

Clinical manifestations (What are the symptoms?)

Persistent diarrhea, abdominal pain, and involuntary loss of weight are the most
common symptoms in RCD.20 Multiple vitamin deficiencies, anemia, fatigue, and
malaise are also frequent.8, 20 Thromboembolic events and coexisting autoimmune
disorders are frequent in RCD.14 The majority of patients with RCD are diagnosed
because of the development of new symptoms or recurrence of diarrhea after
initial clinical response to GFD for years (“secondary” RCD).15, 17 However, a
subgroup of patients is diagnosed because of the necessity of early intervention
to control their symptoms due to lack of response after 6–12 months of GFD
(“primary” RCD).15, 17

Laboratory Findings (What the doctor  may see in lab?)

Low hemoglobin and hypoalbuminemia are frequent findings and may indicate a poor
prognosis