The colonization over time of cystic fibrosis patients by Aspergillus fumigatus was investigated using a DNA fingerprinting method. Aspergillus fumigatus isolates collected sequentially for more than one year from six patients with cystic fibrosis were typed by Southern blot hybridization with a repetitive DNA sequence. Each cystic fibrosis patient harbored several strains of Aspergillus fumigatus that were isolated recurrently over time. Isolates collected from a cystic fibrosis patient with aspergilloma displayed the same genotype, suggesting that the infection was due to a single strain. Continuous isolation of the same genotype in another cystic fibrosis patient, however, was not correlated clinically with an Aspergillus infection.