Development of molecular methods have increased the possibilities in diagnostics. New opportunities as well as limitations of these new methods (PCR, Real-time PCR, sequencing) in the field of clinical microbiology are discussed using a study with Feline Immunodeficiency Virus (FIV) as an example. In this preliminary study (due to the small number of investigated cats) we found an unexpected high degree of serologically FIV positive cats (18.5%). The percentage of positive cats was even higher in the more sensitive PCR (25.9%). In parallel, different other molecular methods for detection and quantification have been employed (Realtime PCR, sequencing) and the advantages and disadvantages are discussed. The findings obtained in this study should be implemented in development of new molecular based assays.