Fluorescence in situ hybridisation (FISH) has gained major impact in the detection of chromosomal aberrations. The application of FISH, however, is hampered due to complicated protocols. We therefore designed a FISH protocol that allows the fast and reliable application on cytological and histological specimens. Cytological and histological specimens of bone marrow, lymph nodes, liver and breast were analysed with 14 sets of centromere or locus-specific probes. A pretreatment of enzymatic digestion and microwave heating with the same incubation times for all specimens and probes used was performed. Hybridisation efficiency was proved by calculating the thresholds for monosomy, trisomy and translocations. Values in cytological specimens reached 9.0, 3.9 and 4.6%, respectively. In histological sections, values of 6.4% were seen for aneusomy and 3.1% for translocations. However, values for monosomy reached 20.5% in bone marrow and 61.8% in liver tissues due to cutting artifacts. In bone marrow with acute myeloid leukaemias, lymph nodes with follicular and mantle cell lymphomas, breast carcinomas and liver cell carcinomas, FISH confirmed aberrations already found using conventional cytogenetics. The protocol shown here is easy to perform and can be used with cytological and histological specimens. Moreover, with "hands on" time of less than 2 h, FISH can also be used for daily routine purposes.