The association between infection with Gram-negative bacteria and autoimmune diseases has been investigated with controversies about the role of the organisms especially, Helicobacter pylori (H. pylori). To evaluate the impact of the presence and activity of H. pylori on the disease activity in patients with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and ankylosing spondylitis (AS). This study was carried out on one hundred adult patients and 50 controls. Patients included 40 RA, 40 SLE, and 20 AS. Participants were subjected to clinical examination and laboratory investigations; ESR (spectrophotometric assay), CRP (turbidimetric method), serum H.pylori IgG antibody test (enzyme immunoassay), and H. pylori antigen test (lateral flow immunoassay, rapid one-step test) in stool. Positive test in stool indicated active current H. pylori infection. Mean age of patients was 36.95±10.34; 51.2±6.91, 35.5±3.71, and 48.82±5.81 in SLE, RA, AS, and control groups respectively. Serum H. pylori IgG antibodies was 0.803±0.497 U/mL in SLE group, 1.48±0.637 U/mL in RA group and 0.75±0.68 U/mL in AS group while it was 0.2±0.61U/mL in the control group with a significant difference (P=0.000). The H. pylori antigen in stool was found positive in 30%, 70% and 20% of patients of the three groups respectively while it was positive in 10% of the control group with P>0.001. Patients with active SLE (SLEDAI >3) and RA (DAS-28 >3.2) demonstrated higher frequency of positive test for H. pylori antigen in stool than patients at remission (66.7% P= 0.02 and 83.3% P= 0.01 respectively). In contrast, 22.2% of patients with active AS (BASDAI > 4) were positive for H. pylori in stool. In conclusion, H. pylori infection is associated with increased disease activity in patients with SLE and RA but not AS.