Protein patterns of nasal lavage fluid (NLF) and bronchoalveolar lavage fluid (BALF) were analyzed with two-dimensional gel electrophoresis (2-DE) and a number of previously unidentified proteins (lipocalin-1, cystatin S, transthyretin, immunoglobulin binding factor and an 11 kDa fragment of albumin) were identified by N-terminal amino acid sequencing. Lipocalin-1 was shown to be a dominant protein in NLF from healthy subjects but was almost undetectable in NLF from a patient with asthma. It further appeared that lipocalin-1 in NLF consists of eight forms with pIs between 5.2 and 5.5: three with the expected Mr of 17500, two with increased Mr (18000), and three truncated variants with Mr of 17000. Two forms of cystatin S were identified both in NLF and BALF: one with pI 5.1 and Mr 13000, and the other with pI4.9 and Mr 13500. The distribution of the two forms was clearly different in NLF and BALF from healthy subjects with the 4.9/13500 form constituting only about 13% in NLF but 69% in BALF. In NLF from subjects with upper airway irritation a twofold increased proportion of the 4.9/13500 form was detected. Amino acid sequence data and the spot position indicate that the 4.9/13500 form might be a phosphorylated variant of cystatin S. Lower levels of both forms of cystatin S were found in BALF from smokers than nonsmokers. The levels of transthyretin in NLF were decreased in subjects exposed to irritating chemicals. Finally, higher levels of IgBF were found in BALF from smokers than nonsmokers. Taken together, these results illustrate the potential biomedical and clinical applications of identifying proteins in 2-DE patterns of human BALF and NLF. The possibility to describe and monitor airway disorders at the molecular level is inferred.