We have invented a high-throughput imaging flow cytometry method that integrates fluorescence in situ hybridisation (FISH) with immunophenotyping on thousands of cells in suspension (“immuno-flowFISH”) in a single automated test. Here we demonstrate the diagnostic utility of immuno-flowFISH on chronic lymphocytic leukaemia (CLL), to detect chromosomal abnormailities that predict prognosis (i.e. trisomy 12 (+12) and del(17p)). Normal blood (n = 20) and diagnostic CLL cases (n = 55) were assessed. Blood mononuclear cells were phenotyped with fluorochrome-conjugated antibodies (CD3, CD5, CD19). Following fixation, membrane permeabilisation and denaturation of nuclear DNA, chromosome 12 enumeration probe (CEP12) or chromosome 17 enumeration probe (CEP17) and 17p12 locus specific FISH probes were added. CEP12 was used to identify cases with +12, present in 15% of CLL, and 17p12 was used to identify rare cases with del(17p), which confers the worst prognostic outcome (3-5% cases); CEP17 was used as an internal control. Up to 20,000 cells were collected on the Amnis ImageStreamX Mark II imaging flow cytometer (ISX MKII). Digital images (x60) and quantitative data were used to assess morphology and FISH probe “spots” in CLL cells identified by CD5+/CD19+/CD3- phenotype (IDEAS software). Sixteen percent (8/50) of cases had three CEP12 spot (+12) signals in cells with the CLL phenotype. The number of cells with +12 ranged from 0.1-45.5%. Ten percent (5/50) of cases had one 17p spot signal ranging from 3.5-22.8% cells with the CLL phenotype; all cells had 2-spots for CEP17. The remaining 42/55 cases had 2-spot patterns for CEP12, 17p and CEP17 in CLL, normal B- and T-cells. All cases were 100% concordant with pre-treatment conventional FISH results. The data demonstrates immuno-flowFISH is a powerful integrated phenotype-genotype method that can analyse large numbers of cells. This significantly increases the accuracy and sensitivity of detection of chromosomal abnormalities over conventional FISH.