Complex karyotype (CK) with ≥3 abnormalities is detected in 10-12% of patients with acute myeloid leukemia (AML) and associated with poor prognosis. The most common unbalanced abnormalities found in CK result in loss of material from the 5q, 7q and/or 17p chromosome arms. The presence of 5q, 7q and/or 17p abnormalities denotes typical CK and their absence denotes atypical CK. Since molecular features of CK-AML are not well-characterized, we investigated mutational status of 81 leukemia/cancer-associated genes in 160 clinically well-characterized patients. They included 136 patients with ≥3 exclusively unbalanced chromosome abnormalities, 96 of whom had a typical CK and 40 atypical CK, and 24 patients with ≥1 balanced abnormality in addition to ≥2 unbalanced ones. Patients with atypical CK-AML differed from those with typical CK-AML: they carried
TP53
mutations less often (
P
<0.001) and more often
PHF6
(
P
=0.008),
FLT3
-TKD (
P
=0.02),
MED12
(
P
=0.02) and
NPM1
(
P
=0.02) mutations. They were younger (
P=
0.007), had higher WBC (
P
=0.001) and percentages of marrow (
P
<0.001) and blood (
P
=0.006) blasts, higher complete remission rates (
P
=0.02) and longer overall survival (
P
<0.001), thus indicating that atypical and typical CK-AMLs constitute distinct disease subtypes. We also identified smaller patient subsets within both typical and atypical CK-AML that differed molecularly and clinically.