To investigate the association between Helicobacter pylori and anemia, a community-based cross-sectional study was conducted among 18-45 year old users of the 31 primary health care units in Pelotas, Southern Brazil. Interviews using a structured questionnaire were carried out in waiting rooms during two work shifts. Anemia (hemoglobin < 11g/dL among pregnant women, < 12g/dL among women and < 13g/dL among men) was diagnosed from capillary blood (HemoCue) and H. pylori by means of a 13C-UBT. Information on socio-demographic, behavioral and biological characteristics was collected. Logistic and linear regression analyses were carried out, taking into account aggregated primary health care units. A total of 1,117 respondents fulfilled the inclusion criteria (losses/refusals: 8.1%). Prevalence of anemia was 20.6% (18.2-23.2%) and of H. pylori, 70.7% (68.0-73.6%). After allowing for age, sex and skin color the odds ratio for anemia among those who were diagnosed H. pylori positive was 0.94 (0.70-1.27). After allowing for sex, skin color, family monthly income, age, and smoking, the reduction in hemoglobin among H. pylori positive respondents was 0.07g/dL (-0.24-0.11; p = 0.4). There is no association between H. pylori and anemia among adults attending primary health care units in Southern Brazil.