Accurate immunophenotyping and cytogenetic analysis of haematological malignancies are essential at diagnosis for deriving appropriate therapeutic strategies. Combining immunophenotyping with fluorescence in situ hybridisation (FISH) in a single test (e.g. FICTION) enables genetic abnormalities to be directly assessed in neoplastic cells identified by phenotype, improving sensitivity. Currently, FISH performed manually on intact cells in cell smears or tissue sections. This is labour intensive, time consuming and has low sensitivity with only 100-200 cells analysed. This is not suitable when the number of neoplastic cells is low or for ongoing disease monitoring of rare events. Image-based flow cytometry combines high resolution digital images with the quantitative fluorescence information gained from a standard flow cytometer, in a single platform. The imaging functionality allows the localisation of FISH probe signals or “spots” to be localised within the nucleus of cells, a feature that cannot be achieved by standard flow cytometry. We have developed an imaging flow cytometry method whereby FISH is integrated with cell phenotyping (“immuno-flowFISH”) on cells in suspension. This method was developed on normal peripheral blood lymphocytes and involved validation of a number of FISH probes, fluorophores and immunophenotyping antibody clones. We have assessed chronic lymphocytic leukaemia (CLL) blood samples and bone marrow aspirates from paediatric acute lymphoblastic leukaemia (ALL) and multiple myeloma cases, where we successfully detected numeric (e.g. +12) and structural (e.g. del(17p)) chromosomal abnormalities in phenotyped cells. This new method enables FISH probe signals to be analysed in a large number of cells in suspension at high throughput, providing accurate analysis of chromosomal abnormalities to low detection levels. It is therefore suitable for minimal residual disease analysis, in contrast to traditional slide-based FISH.