FLT3-internal tandem duplication (ITD) mutations are heterogeneous with regards to length and proportion of DNA harbouring the mutation and the expression level of FLT3 also varies widely, however very little is known about the biological effects of these variables. We studied FLT3-associated biological parameters in 322 acute myeloid leukaemia samples to establish their importance. Expression of total FLT3 transcripts was shown to be significantly higher in the FLT3-ITD cohort (n = 121) compared to the wild-type cohort (P = 0.004). Whilst phosphorylated signal transducer and activator of transcription 5 (phospho-STAT5) was not confined to FLT3-ITD samples, within the FLT3-ITD group phosphorylation correlated with adjusted FLT3-ITD levels assessed by determining the total transcripts and proportion of FLT3-ITD within a sample. Expression of the STAT5 downstream target Bcl-xl (an isoform of BCL2L1) was strongly correlated with FLT3 total and adjusted FLT3-ITD levels in FLT3-ITD samples (P < 0.001), however there was no association between Bcl-xl and phospho-STAT5 levels suggesting that STAT5 is not the sole regulator of Bcl-xl in FLT3-ITD cells. We further stratified our cohort by the presence/absence of a cytoplasmic nucleophosmin NPMc+ mutation. Samples co-expressing NPMc+ had longer FLT3-ITD mutations (P = 0.01) and there was a high occurrence of NPMc+ in samples that had >1 FLT3-ITD mutation. Phospho-STAT5 levels were reduced in the FLT3-ITD/NPMc+ group (P = 0.04) suggesting that NPMc+ may oppose the FLT3-ITD-dependent activation of STAT5.