We investigated the presence of anti-neutrophil cytoplasmic antibodies (ANCA) in the serum and bronchoalveolar lavage fluid (BALF) of 21 cystic fibrosis (CF), 7 idiopathic bronchiectasis (IBR), and 11 control children and the relation between ANCA and any bacteria grown in BALF. Six of the CFs, but none of the IBRs or controls had positive serum cytoplasmic or perinuclear-ANCA (c-ANCA, p-ANCA). Serum autoantibodies against bactericidal/permeability increasing protein (BPI-ANCA) were positive in 2 CFs, 1 IBR and 1 control. While none of the CFs, IBRs or controls had positive BALF (c- or p-ANCA), 1 CF, 1 IBR and none of the controls had positive BALF BPI-ANCA. Pseudomonas aeruginosa was not grown in the specimens of any of the subjects. As the number of the patients in our study was very limited, further longitudinal and well-designed studies are necessary to show whether or not the presence of ANCA in serum or BALF relates to the presence of P. aeruginosa infection in the airways of CF and IBR patients.