We investigated the prevalence of bacterial and parasitic infections among workers in a pastry factory in North Lebanon in 2004. We found 39% of the workers (n = 196) had nasal carriage of Staphylococcus aureus. Resistance of S. aureus isolates was 98.7% to penicillin G, 24.7% to fusidic acid, 14.3% to pefloxacine and tetracycline, 11.7% to erythromycin, 6.5% to oxacillin and amoxicillin–clavulanate. Salmonella typhi was not found in any of the workers. Prevalence of intestinal parasites was 57.8% (n = 308). Amoebae comprised 72.5% (68.3% Entamoeba coli, 15.5% E. histolytica), followed by flagellates (18.0 %) (37.5% Dientamoeba fragilis, 31.3% Giardia lamblia) and nematodes (7.8%) (only Ascaris lumbricoides). The tuberculin test was positive in 16.3% of the workers (n = 301).