To analyse the influence of antibiotic therapy on the faecal flora of patients from general practice with complaints of a respiratory tract infection (RTI), 189 paired faecal specimens were collected, before and after completing antibiotic treatment (n = 129) and symptomatic treatment (n = 60). Faecal specimens were examined for the prevalence and degree of resistance to amoxycillin, apramycin, ciprofloxacin, nalidixic acid, neomycin, nitrofurantoin, oxytetracycline, sulphamethoxazole and trimethoprim. In the antibiotic-treated group a significant increase in the prevalence of resistance to amoxycillin post-treatment from 50% to 64% (P < 0.05, Wilcoxon) was observed. In the symptomatic treated group no significant differences in the prevalence of resistance were found. Using discriminant analysis, amoxycillin and doxycycline therapy contributed to an increased prevalence of resistance to amoxycillin and oxytetracycline, respectively. In the antibiotic-treated group Escherichia coli isolates post-treatment had a significantly increased resistance rate to amoxycillin (15%-23%) and to neomycin (2%-6%) (P < 0.05, Wilcoxon). Logistic regression analysis showed a cross resistance to neomycin and kanamycin, and for kanamycin cross-resistance to apramycin, neomycin and streptomycin occurred.