T-cell acute lymphoblastic leukemia (T-ALL) is a biologically heterogeneous malignancy, which reflects distinctive stages of T-cell differentiation arrest. We have revisited a cohort of pediatric T-ALL, in order to test if immunophenotypes associated with molecular alterations would predict the patient's outcome. Genetic mutations, translocations and copy number alterations were identified through Sanger sequencing, RT-PCR, FISH and multiplex ligation-dependent probe amplification (MLPA). We defined 8 immunophenotypic T-ALL subtypes through multiparametric flow cytometry: early T-cell precursor (ETP,
n
= 27), immature (
n
= 38), early cortical (
n
= 15), cortical (
n
= 50), late cortical (
n
= 53), CD4/CD8 double negative mature (
n
= 31), double positive mature (
n
= 35) and simple positive mature (
n
= 31) T-ALL. Deletions (del) or amplifications (amp) in at least one gene were observed in 87% of cases. The most frequent gene alterations were
CDKN2A/B
del
(71.4%),
NOTCH1
mut
(47.6%) and
FBXW7
mut
(17%). ETP-ALL had frequent
FLT3
mut
(22.2%) and
SUZ12
del
(16.7%) (
p
< 0.001), while
CDKN2A/B
del
were rarely found in this subtype (
p
< 0.001). The early cortical T-ALL subtype had high frequencies of
NOTCH1
mut
and
IL7R
mut
(71%, 28.6%, respectively), whereas, mature T-ALL with double positive CD4/CD8 had the highest frequencies of
STIL-TAL1
(36.7%),
LEF1
del
(27.3%) and
CASP8AP2
del
(22.7%). The co-existence of two groups of T-ALL with
NOTCH1
mut
/IL7R
mut
, and with
TLX3/SUZ12
del
/NF1
del
/
IL7R
mut
, were characterized with statistical significance (
p
< 0.05) but only
STIL-TAL1
(pOS 47.5%) and
NOTCH1
WT
/
FBXW7
WT
(pOS 55.3%) are predictors of poor T-ALL outcomes. In conclusion, we have observed that 8 T-ALL subgroups are characterized by distinct molecular profiles. The mutations in
NOTCH1/FBXW7
and
STIL-TAL1
rearrangement had a prognostic impact, independent of immunophenotype.