Acute lymphoblastic leukemia (ALL) is a complex genetic disease involving many fusion oncogenes having prognostic significance. The frequency of various fusion oncogenes can vary in different ethnic groups, with important implications for prognosis, drug selection and treatment outcome. We studied fusion oncogenes in 101 pediatric ALL patients using RT-PCR and interphase FISH, and their associations with clinical features and treatment outcome. Five most common fusion genes i.e. BCR-ABL t (22; 9), ETV6-RUNX1 (t 12; 21), MLL-AF4 (t 4; 11) TCF3-PBX1 (t 1; 19), and SIL-TAL1 (del 1p32) were found in 88.1% (89/101) patients. Frequency of BCR-ABL was 44.5% (45/101). BCR-ABL positive patients had a significantly lower survival (43.7±4.24 weeks) and higher white cell count as compared to others, except patients with MLL-AF4. The highest relapse-free survival was documented with ETV6-RUNX1 (14.2 months) followed closely by those cases in which no gene was detected (13.100). RFS with BCR-ABL, MLL-AF4, SIL-TAL1 and TCF3-PBX1 was less than 10 months (8.0, 3.6, 5.5 and 8.1 months, respectively). This is the first study from Pakistan correlating molecular markers with disease biology and treatment outcome in pediatric ALL. It revealed the highest reported frequency of BCR-ABL fusion gene in pediatric ALL, associated with poor overall survival. Present data indicated an immediate need for incorporation of tyrosine kinase inhibitors in the treatment of BCR-ABL+ pediatric ALL in this population and the development of facilities for stem cell transplantation.