SETTING: Malnutrition and intestinal parasites cause immunosuppression. This may cause false-negative tuberculin skin tests (TST) and failure to identify tuberculosis (TB) infection. OBJECTIVE: To assess factors associated with TST positivity and anergy in disadvantaged communities in Peru. DESIGN: A study of 212 randomly selected adults: 102 in a rural Amazonian village and 110 shanty town residents in urban Lima. RESULTS: Respectively 52% and 53% of urban and rural jungle populations were TST-positive. Using simultaneous tetanus and candida skin tests, 99% had at least one positive skin test. Generalised anergy was therefore rare, despite frequent intestinal parasitic infection, including 34% helminth infection prevalence in the jungle. TST positivity was associated with age (P = 0.001), known TB contact (P = 0.02) and poor household ventilation (P = 0.007). TST positivity was not significantly associated with crowding, reported past TB, single/multiple BCG vaccination, income, intestinal parasites, dietary factors, body mass index or body fat. Individuals with lower anthropometric body protein, as measured by corrected arm muscle area, were less likely to be TST-positive (P = 0.02), implying that protein malnutrition caused tuberculin-specific anergy. CONCLUSION: These results identify the importance of household ventilation for community TB transmission and add to the evidence that protein malnutrition suppresses TB immunity, causing false-negative TST results.