We have previously identified an allele of the human SP-A2 gene that occurs with greater frequency in an RDS population [12]. Because of the importance of SP-A in normal lung function and its newly emerging role in innate host defense and regulation of inflammatory processes, we wish to better characterize genotypes of both SP-A1 and SP-A2 genes. It has been determined that SP-D shares similar roles in immune response. Therefore, in this report we 1) describe a novel, non radioactive PCR based-cRFLP method for genotyping both SP-A and SP-D; 2) describe two previously unpublished biallelic polymorphisms within the SP-D gene; 3) present the partial sequence of one new SP-A1 allele (6A14) and describe other new SP-A1 and SP-A2 alleles; and 4) describe additional methodologies for SP-A genotype assessment. The ability to more accurately and efficiently genotype samples from individuals with various pulmonary diseases will facilitate population and family based association studies. Genetic polymorphisms may be identified that partially explain individual disease susceptibility and/or treatment effectiveness.