In this study a highly sensitive detection method for Mycobacterium avium subspecies paratuberculosis (M. ptb) in milk and colostrum via a capture PCR using peptides linked to paramagnetic beads was developed. Primers were derived from the M.ptb specific insertion sequence ISMav2. Using a library of filamentous phages expressing random 12-mer peptides on their surface, it was possible to initially select nine clones that bind to M. ptb. Selection of these clones was performed during five rounds of biopanning, with whole M. ptb as target, in the last round washing buffers containing 4M guanidine hydrochloride or 6M urea were used. The specificity of the clones derived was confirmed via fluorescence microscopy and in a plate binding assay. For the fluorescence microscopy the phages were conjugated with FITC to visualize binding to M. ptb. In the plate binding assay M. ptb was coated onto microtiter plates and bound phages were detected using streptavidin alkaline phosphatase as conjugate. This led to the selection of two specific phages. The amino acid sequences of the binding petides were deduced via DNA sequencing and the peptides expressed on these phages were synthesized with an N-terminal biotinylation using amino-hexa-carbone-acid as spacer. By linking the peptides to streptavidin coated paramagnetic beads it was possible to enrich M. ptb in milk. Subsequent processing envolved boiling and DNA purification with the Gene clean(r) Kit. The final PCR reproducibly allowed for the detection of 10² M. ptb per milliliter milk. Using this method it was possible to detect M. ptb in milk from naturally infected cows in the diagnostic laboratory.